Contacts of the helix formed by residues 93 - 107 (chain A) in PDB entry 4H7Y
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 PHE 93 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A GLY 4.1 5.6 - - - -
56A GLN 3.4 32.1 - - - -
57A ASN 4.0 9.9 - - - -
58A GLU* 3.7 32.5 - - + -
61A ALA* 3.7 15.0 - - + -
90A CYS* 3.4 11.6 + - + -
91A LYS 3.2 1.8 - - - -
92A LYS* 1.3 110.8 - - + +
94A ALA* 1.3 65.4 + - - +
95A PHE* 3.8 29.4 - + + -
96A VAL* 3.0 17.7 + - + +
97A HIS* 3.2 14.7 - - - -
126A VAL* 3.7 7.4 - - + -
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Residues in contact with ALA 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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92A LYS 3.6 2.0 + - - -
93A PHE* 1.3 71.1 - - - +
95A PHE* 1.3 62.6 + - - +
96A VAL 3.1 0.5 + - - -
97A HIS* 3.2 5.7 + - - +
98A ILE* 3.0 27.6 + - + +
125A ALA* 4.1 9.2 - - - -
126A VAL 2.8 26.6 + - - +
127A PRO* 3.5 24.5 - - + +
130A MET* 4.2 8.3 - - + -
131A LEU* 3.8 20.2 - - + -
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Residues in contact with PHE 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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58A GLU* 4.3 14.8 - - + -
61A ALA* 3.6 24.0 - - + -
62A ARG* 3.7 27.4 - - + -
65A VAL* 3.8 31.9 - - + -
93A PHE* 3.2 32.7 - + + -
94A ALA* 1.3 79.5 - - - +
96A VAL* 1.3 57.3 + - + +
98A ILE* 3.9 5.0 - - - +
99A SER* 3.0 28.8 + - - -
127A PRO* 5.6 0.4 - - - +
130A MET* 3.9 24.9 - - + +
146A LEU* 5.9 1.8 - - + -
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Residues in contact with VAL 96 (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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61A ALA* 4.0 17.5 - - + +
65A VAL* 3.7 20.9 - - + +
83A PHE* 5.0 1.7 - - - +
86A ALA* 3.7 14.6 - - + +
87A ARG* 3.6 38.1 - - + +
90A CYS* 3.9 13.9 - - + +
93A PHE* 3.0 27.4 + - + +
95A PHE* 1.3 79.1 - - + +
97A HIS* 1.3 67.0 + - + +
99A SER* 3.4 4.7 + - - -
100A PHE* 3.2 20.3 + - - +
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Residues in contact with HIS 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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87A ARG* 3.6 36.6 + - + +
91A LYS* 2.7 33.6 + - + -
93A PHE 3.2 25.4 - - - -
94A ALA 3.2 4.4 + - - +
96A VAL* 1.3 79.1 - - + +
98A ILE* 1.3 58.2 + - - +
100A PHE* 3.3 8.8 + - - +
101A ALA* 2.8 27.9 + - - +
116A LEU* 4.5 13.2 + - + +
117A LEU* 4.6 1.3 - - + +
119A LYS* 6.1 0.6 - - + +
120A ALA* 3.5 35.0 - - + +
123A ARG* 5.3 13.0 - - + -
125A ALA* 3.7 14.5 - - + +
131A LEU* 4.7 2.2 - - + -
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Residues in contact with ILE 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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94A ALA 3.0 18.0 + - - +
95A PHE* 3.9 4.3 - - - +
97A HIS* 1.3 74.5 - - - +
99A SER* 1.3 55.3 + - - +
101A ALA* 3.6 0.9 - - - +
102A GLN* 2.7 36.0 + - + +
117A LEU* 3.6 23.6 - - + -
130A MET* 3.4 52.7 - - + +
131A LEU* 3.8 9.9 - - + -
134A ALA* 4.1 2.7 - - + -
145A LEU* 4.2 17.9 - - + -
146A LEU* 4.1 24.0 - - + +
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Residues in contact with SER 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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65A VAL* 3.4 18.5 - - - +
69A GLU* 2.7 28.2 + - - +
83A PHE* 3.2 25.6 - - - -
95A PHE* 3.0 18.7 + - - -
96A VAL 3.4 5.8 + - - -
98A ILE* 1.3 77.8 - - - +
100A PHE* 1.3 60.5 + - - +
102A GLN* 3.3 7.2 + - - +
103A PHE 3.0 19.1 + - - -
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Residues in contact with PHE 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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80A ARG* 4.1 11.0 - - + -
83A PHE* 3.4 40.9 - + + +
84A GLN* 3.4 42.6 - - + -
87A ARG* 3.9 26.5 - - + -
96A VAL 3.2 10.1 + - - +
97A HIS* 3.4 10.3 - - - +
98A ILE 3.2 0.2 - - - -
99A SER* 1.3 76.5 - - - +
101A ALA* 1.3 63.6 + - - +
103A PHE* 3.2 6.1 + + - +
104A GLU* 3.0 46.1 + - + +
112A LYS* 5.5 4.3 - - - -
116A LEU* 3.7 27.6 - - + -
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Residues in contact with ALA 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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97A HIS 2.8 17.4 + - - +
98A ILE 3.2 1.8 + - - +
100A PHE* 1.3 77.2 - - - +
102A GLN* 1.3 56.4 + - - +
104A GLU 3.4 0.5 + - - -
105A LEU* 3.0 19.2 + - - +
113A SER* 2.8 32.4 + - - +
116A LEU* 3.9 13.9 - - + +
117A LEU* 3.7 21.3 - - + -
145A LEU* 3.5 18.8 - - + -
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Residues in contact with GLN 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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69A GLU* 6.1 0.4 - - - +
98A ILE* 2.7 22.1 + - + +
99A SER* 3.5 9.0 - - - +
100A PHE 3.3 0.2 - - - -
101A ALA* 1.3 71.2 - - - +
103A PHE* 1.3 64.7 + - - +
105A LEU* 3.7 5.7 - - - +
106A SER* 2.9 30.4 + - - +
143A LYS 3.0 23.2 + - - -
144A GLN* 3.1 20.1 + - - +
145A LEU* 2.8 39.5 + - + +
146A LEU 4.6 1.2 + - - -
33B ALA* 6.1 1.3 - - + -
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Residues in contact with PHE 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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72A ALA* 3.9 15.3 - - + -
76A PRO* 3.5 27.1 - - + -
79A ALA* 4.1 10.1 - - + -
80A ARG* 3.8 50.9 - - + -
83A PHE* 3.5 39.0 - + + -
99A SER 3.0 7.1 + - - +
100A PHE* 3.4 10.8 - + - +
102A GLN* 1.3 77.4 - - - +
104A GLU* 1.3 72.8 + - - +
106A SER* 2.8 25.3 + - - -
107A GLN* 3.1 35.8 + - + +
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Residues in contact with GLU 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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80A ARG* 2.5 37.4 + - - -
100A PHE* 3.0 32.7 + - + +
101A ALA 3.9 4.3 - - - +
103A PHE* 1.3 79.9 - - - +
105A LEU* 1.3 60.9 + - - +
107A GLN* 3.1 8.6 + - - +
109A ASN* 2.8 70.0 + - + +
112A LYS* 3.8 17.2 - - + +
113A SER* 4.1 8.1 - - - +
116A LEU* 3.6 18.2 - - + -
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Residues in contact with LEU 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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101A ALA 3.0 18.2 + - - +
102A GLN* 3.7 5.6 - - - +
104A GLU* 1.3 76.7 - - - +
106A SER* 1.3 56.5 + - - +
108A GLY* 2.8 22.2 + - - -
109A ASN 4.4 3.1 - - - +
110A VAL* 3.8 26.2 - - + -
113A SER* 3.7 9.5 - - - +
138A LEU* 3.9 15.9 - - + -
141A GLN* 6.5 0.7 - - - -
142A LYS 3.7 17.3 - - - +
143A LYS* 3.6 24.5 - - - +
145A LEU* 3.9 28.7 - - + -
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Residues in contact with SER 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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102A GLN* 2.9 23.1 + - - +
103A PHE* 2.8 24.8 + - - -
105A LEU* 1.3 76.7 - - - +
107A GLN* 1.3 73.6 + - - +
108A GLY 3.2 1.4 + - - -
143A LYS 6.0 0.2 - - - -
32B ASP* 4.5 19.5 + - - +
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Residues in contact with GLN 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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76A PRO* 4.0 25.3 - - - +
77A ASP* 4.4 9.4 - - - +
80A ARG* 4.8 3.8 - - - +
103A PHE* 3.1 44.0 + - + +
104A GLU* 3.6 7.6 - - - +
105A LEU 3.1 1.0 - - - -
106A SER* 1.3 99.4 + - - +
108A GLY* 1.3 60.1 + - - +
109A ASN* 3.3 19.5 + - - +
32B ASP* 6.3 0.8 - - - -
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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