Contacts of the helix formed by residues 93 - 114 (chain A) in PDB entry 4NZP
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 93 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A MET* 3.6 27.4 - - - -
85A ALA* 3.9 26.9 - - + +
87A TYR* 3.8 14.1 - - + +
91A TYR* 3.2 24.7 - - + +
92A LEU* 1.3 77.1 - - - +
94A GLY* 1.3 64.7 + - - +
95A THR 3.3 3.1 - - - -
96A SER* 3.4 10.0 + - - +
97A ILE* 3.0 24.4 + - - +
314A ALA* 3.6 34.3 - - + +
317A ILE* 4.2 5.6 - - + -
318A TYR* 3.8 26.5 - - + +
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Residues in contact with GLY 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A TYR* 3.4 6.9 + - - -
92A LEU* 3.1 4.2 + - - +
93A LEU* 1.3 76.0 - - - +
95A THR* 1.3 61.2 + - - +
97A ILE* 3.8 5.4 - - - +
98A ALA* 3.7 5.9 - - - +
185A ASN* 2.8 20.4 + - - -
187A LEU* 3.8 20.4 - - - -
188A HIS* 3.5 27.5 - - - -
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Residues in contact with THR 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A TYR* 3.0 11.9 + - - -
94A GLY* 1.3 73.8 - - - +
96A SER* 1.3 68.1 - - - +
98A ALA* 3.2 12.7 + - - +
99A ARG* 3.3 26.6 + - + +
128A ASP* 3.8 12.3 - - - +
131A ARG* 3.7 22.9 - - - +
183A ASP* 3.4 24.6 + - + +
185A ASN* 4.5 0.2 - - - +
188A HIS* 3.1 20.3 + - - -
190A SER* 4.4 4.3 + - - -
278A TYR* 4.8 1.6 - - - -
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Residues in contact with SER 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A TYR* 3.9 10.7 - - - -
93A LEU* 3.4 6.7 + - - +
95A THR* 1.3 78.4 - - - +
97A ILE* 1.3 56.5 + - - +
99A ARG* 3.8 2.6 + - - +
100A PRO* 3.1 22.0 - - - +
131A ARG* 3.2 32.2 + - - +
317A ILE* 3.5 34.9 - - - +
318A TYR* 3.6 20.4 - - - -
320A GLY* 5.9 0.7 - - - -
322A TRP* 5.8 0.7 - - - +
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Residues in contact with ILE 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A PHE* 3.9 13.6 - - + -
76A TYR* 3.5 46.0 - - + +
77A VAL* 4.2 1.6 - - + +
80A MET* 3.9 19.1 - - + -
93A LEU 3.0 21.8 + - - +
94A GLY 3.8 5.2 - - - +
96A SER* 1.3 78.1 - - - +
98A ALA* 1.3 64.2 + - - +
100A PRO* 3.3 15.1 - - + +
187A LEU* 3.7 24.7 - - + -
317A ILE* 4.3 8.1 - - + -
322A TRP* 3.7 35.0 - - + -
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Residues in contact with ALA 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ILE* 3.9 17.1 - - + +
72A PHE* 3.4 21.1 - - + -
94A GLY 3.7 2.7 + - - +
95A THR 3.2 5.2 + - - +
97A ILE* 1.3 81.7 - - - +
99A ARG* 1.3 72.1 + - - +
101A LEU* 3.3 14.9 + - - +
102A ILE* 3.4 14.6 + - - +
185A ASN* 3.5 28.7 - - - +
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Residues in contact with ARG 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ILE* 5.2 2.8 - - - +
95A THR* 3.3 24.1 + - - +
96A SER 4.0 0.7 - - - +
98A ALA* 1.3 82.2 - - - +
100A PRO* 1.4 68.8 - - + +
102A ILE* 3.0 23.9 + - - +
103A ALA* 3.0 22.9 + - - +
128A ASP* 2.9 34.2 + - - +
131A ARG* 3.5 44.2 - - + -
132A PHE* 3.9 28.6 - - + +
183A ASP* 3.1 37.0 + - - +
185A ASN* 5.6 0.2 - - - +
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Residues in contact with PRO 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A TYR* 4.1 2.7 - - + -
96A SER 3.1 18.6 - - - +
97A ILE* 3.3 17.3 - - - +
99A ARG* 1.4 92.1 - - + +
101A LEU* 1.3 60.3 + - - +
103A ALA* 4.0 6.2 - - + +
104A LYS* 3.0 27.9 + - - +
131A ARG* 5.3 4.7 - - + +
135A GLY* 5.6 1.8 - - - -
320A GLY* 6.5 1.1 - - - -
322A TRP* 3.7 34.5 - - + -
323A PHE* 3.4 26.9 - - + -
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Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ILE* 3.9 12.6 - - + -
68A LEU* 3.8 25.4 - - + +
71A GLU* 3.7 23.1 - - - +
72A PHE* 3.6 39.0 - - + +
76A TYR* 3.4 40.3 - - + +
98A ALA 3.3 11.1 + - - +
99A ARG 3.2 0.2 - - - -
100A PRO* 1.3 81.9 - - - +
102A ILE* 1.3 58.0 + - - +
104A LYS* 4.0 1.6 - - + +
105A THR* 2.5 42.5 + - - +
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Residues in contact with ILE 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ALA* 5.1 5.4 - - + -
36A PHE* 3.6 22.6 - - + -
38A ALA* 4.9 10.5 - - + -
40A ILE* 3.7 37.7 - - + -
42A GLN* 6.1 0.9 - - - +
68A LEU* 5.4 0.9 - - + -
98A ALA 3.8 12.1 - - - +
99A ARG* 3.0 27.0 + - - +
101A LEU* 1.3 78.5 - - + +
103A ALA* 1.3 55.7 + - - +
105A THR* 3.3 2.4 + - - -
106A GLN* 2.9 32.5 + - - +
132A PHE* 3.6 24.9 - - + -
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Residues in contact with ALA 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ARG 3.0 14.3 + - - +
100A PRO* 4.0 2.7 - - + +
101A LEU 3.4 0.2 - - - -
102A ILE* 1.3 76.6 - - - +
104A LYS* 1.3 58.1 + - - +
106A GLN 3.5 0.2 + - - -
107A ALA* 3.0 28.2 + - - +
131A ARG 4.4 1.6 - - - +
132A PHE* 3.4 39.0 - - + +
135A GLY* 3.9 14.6 - - - -
136A TYR* 3.4 22.3 - - + -
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Residues in contact with LYS 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A GLU* 3.9 18.5 + - - +
76A TYR* 3.4 20.7 + - - +
100A PRO 3.0 17.9 + - - +
101A LEU* 4.0 2.7 - - + +
103A ALA* 1.3 74.1 - - - +
105A THR* 1.3 69.2 + - - +
107A ALA* 3.2 4.0 + - - +
108A GLN* 3.0 51.3 + - - +
135A GLY 5.0 0.4 + - - -
139A PHE* 3.4 54.2 - - + -
323A PHE* 3.9 3.0 - - + -
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Residues in contact with THR 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A PHE* 3.8 26.2 - - + -
66A LYS* 4.2 17.5 - - + -
68A LEU* 3.5 22.8 - - + +
71A GLU* 5.2 1.0 + - - -
101A LEU* 2.5 29.2 + - - +
102A ILE 3.8 3.1 - - - -
104A LYS* 1.3 79.8 - - - +
106A GLN* 1.3 63.5 + - - +
108A GLN* 3.3 14.1 + - + +
109A ILE* 3.0 26.8 + - + +
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Residues in contact with GLN 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A VAL* 2.9 35.2 + - + +
11A ALA* 3.4 24.2 - - - +
36A PHE* 3.8 15.6 - - + -
102A ILE* 2.9 19.2 + - - +
103A ALA 3.8 4.7 - - - +
105A THR* 1.3 79.3 - - - +
107A ALA* 1.3 60.6 + - - +
109A ILE* 3.5 5.9 + - - +
110A ALA* 3.1 22.3 + - - +
118A VAL* 3.7 5.7 - - + +
119A SER 2.8 31.1 + - - +
132A PHE* 4.5 4.0 - - - -
136A TYR* 2.7 29.1 + - + -
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Residues in contact with ALA 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ALA 3.0 18.4 + - - +
104A LYS* 3.2 6.5 + - - +
106A GLN* 1.3 76.7 - - - +
108A GLN* 1.3 58.0 + - - +
110A ALA* 3.3 4.5 - - - +
111A LEU* 3.1 30.7 + - - +
118A VAL* 4.8 0.7 - - - -
136A TYR* 4.1 17.2 - - + +
139A PHE* 3.9 22.7 - - + -
140A SER* 4.5 2.0 - - - -
143A LEU* 4.1 20.1 - - + +
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Residues in contact with GLN 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A LYS* 3.0 52.5 + - + +
105A THR* 3.7 12.5 - - + +
107A ALA* 1.3 76.9 - - - +
109A ILE* 1.3 60.6 + - + +
111A LEU* 3.5 14.5 - - + +
112A GLN* 2.8 31.8 + - - +
139A PHE* 4.1 15.4 - - + -
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Residues in contact with ILE 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A VAL* 4.2 17.7 - - + -
34A VAL* 4.2 1.1 - - + -
36A PHE* 3.4 38.1 - - + -
64A PHE* 3.9 41.3 - - + -
66A LYS* 3.9 28.5 - - + -
105A THR* 3.0 21.6 + - + +
106A GLN 3.8 4.0 - - - +
108A GLN* 1.3 75.4 - - + +
110A ALA* 1.3 57.9 + - - +
112A GLN* 3.3 9.4 + - - +
113A THR* 2.8 37.5 + - + +
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Residues in contact with ALA 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A VAL* 3.5 21.3 - - + +
106A GLN 3.1 15.2 + - - +
107A ALA 3.3 10.8 - - - +
109A ILE* 1.3 77.1 - - - +
111A LEU* 1.3 56.7 + - - +
113A THR* 3.3 1.0 + - - -
114A GLY 3.0 6.9 + - - -
115A ALA* 2.7 36.4 + - + +
118A VAL* 3.9 16.8 - - + -
143A LEU* 4.0 17.0 - - + -
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Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ALA 3.1 20.1 + - - +
108A GLN* 3.5 18.8 - - + +
109A ILE 3.3 0.2 - - - -
110A ALA* 1.3 75.2 - - - +
112A GLN* 1.3 63.3 + - - +
114A GLY* 3.3 12.4 + - - -
115A ALA 5.2 1.6 - - - +
139A PHE* 3.9 21.8 - - + +
140A SER* 3.4 22.7 - - - +
143A LEU* 5.7 2.2 - - + -
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Residues in contact with GLN 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A PHE* 3.5 35.2 - - - -
66A LYS* 5.4 4.5 + - - +
108A GLN 2.8 17.2 + - - +
109A ILE* 3.3 12.5 + - - +
111A LEU* 1.3 80.4 - - - +
113A THR* 1.3 61.5 + - + +
114A GLY 3.5 0.3 + - - -
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Residues in contact with THR 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LYS* 2.5 40.9 + - - +
9A VAL* 4.1 3.5 - - - +
34A VAL* 4.4 6.4 - - + +
61A GLU 5.5 0.4 - - - +
62A ASN* 5.3 3.1 - - - +
64A PHE* 3.6 37.2 - - + -
109A ILE* 2.8 31.1 + - + +
110A ALA* 3.3 7.3 + - - -
112A GLN* 1.3 75.7 - - + +
114A GLY* 1.3 56.8 + - - +
115A ALA* 3.4 15.1 - - - +
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Residues in contact with GLY 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LYS* 4.6 5.7 - - - +
110A ALA 3.0 5.1 + - - -
111A LEU* 3.3 7.3 + - - -
112A GLN 3.3 4.8 + - - -
113A THR* 1.3 78.3 - - - +
115A ALA* 1.3 64.5 + - - +
116A ASP* 3.6 7.8 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il