Contacts of the helix formed by residues 95 - 114 (chain A) in PDB entry 4F2N
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 SER 95 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A THR* 3.9 29.4 - - - +
92A ILE* 2.9 24.3 + - - +
94A GLU* 1.3 80.8 + - - +
96A LYS* 1.3 57.1 + - - +
97A VAL 3.3 2.9 - - - -
98A MET* 3.3 16.5 + - - +
99A PHE* 3.0 29.4 + - - +
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Residues in contact with LYS 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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92A ILE 3.4 4.3 + - - +
93A ASN* 3.4 18.8 + - - +
94A GLU 3.6 1.4 - - - -
95A SER* 1.3 75.5 - - - +
97A VAL* 1.3 61.5 + - + +
99A PHE* 3.6 6.8 - - - +
100A ASN* 3.0 39.7 + - - +
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Residues in contact with VAL 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LYS* 4.4 14.8 - - - -
73A LEU* 3.8 20.2 - - + -
94A GLU 5.4 0.6 + - - -
95A SER 3.3 0.6 - - - -
96A LYS* 1.3 78.6 - - + +
98A MET* 1.3 63.6 + - - +
100A ASN* 3.3 7.6 + - - +
101A GLN* 3.1 34.7 + - - +
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Residues in contact with MET 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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70A LEU* 4.0 15.5 - - + -
73A LEU* 3.5 48.1 - - + +
74A GLY* 4.0 9.2 - - - -
77A TYR* 4.5 16.2 - - + +
85A ILE* 4.1 18.2 - - + -
89A THR* 3.8 20.9 - - + -
95A SER* 3.3 18.5 + - - +
97A VAL* 1.3 75.3 - - - +
99A PHE* 1.3 66.9 + - - +
101A GLN* 3.2 2.9 + - - +
102A ALA* 2.9 23.0 + - - +
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Residues in contact with PHE 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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86A ILE* 3.7 26.9 - - + -
89A THR* 3.4 30.1 + - - +
90A THR* 3.7 32.1 - - - -
95A SER 3.0 16.5 + - - +
96A LYS* 3.6 7.2 - - - +
98A MET* 1.3 77.1 - - - +
100A ASN* 1.3 73.8 + - - +
102A ALA* 3.9 2.6 - - - +
103A ALA* 2.8 52.1 + - + +
176A ALA* 4.3 13.5 - - + -
177A GLY* 4.8 8.5 - - - -
178A CYS* 5.0 2.2 - - + -
181A THR* 4.2 7.6 - - + -
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Residues in contact with ASN 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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96A LYS* 3.0 25.6 + - - +
97A VAL* 3.6 7.3 - - - +
98A MET 3.3 0.2 - - - -
99A PHE* 1.3 91.1 - - - +
101A GLN* 1.3 62.9 + - - +
104A GLN* 3.0 36.2 + - - +
175A ASN* 5.7 0.2 - - - +
176A ALA* 3.6 12.9 + - - +
152B PHE* 3.3 50.0 - - + +
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Residues in contact with GLN 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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65A ALA 4.1 0.9 - - - +
66A TYR* 3.3 38.6 - - - +
69A LYS* 3.3 40.1 - - + +
70A LEU* 3.8 24.2 - - + +
73A LEU* 4.4 5.4 - - + -
97A VAL* 3.1 27.3 + - + +
98A MET* 3.2 3.8 + - - +
100A ASN* 1.3 81.2 - - - +
102A ALA* 1.3 61.6 + - - +
104A GLN* 3.3 2.1 + - - +
105A HIS* 2.9 31.2 + - - +
152B PHE* 4.8 5.7 - - - -
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Residues in contact with ALA 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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70A LEU* 3.9 19.0 - - + +
82A ILE* 3.2 18.2 - - + +
85A ILE* 3.7 28.0 - - + -
86A ILE* 3.9 14.6 - - + +
98A MET 2.9 16.8 + - - +
99A PHE* 3.9 2.2 - - - +
101A GLN* 1.3 76.6 - - - +
103A ALA* 1.3 58.4 + - - +
105A HIS* 3.3 0.9 + - - +
106A PHE* 2.9 25.5 + - - +
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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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86A ILE* 3.7 17.6 - - + +
99A PHE* 2.8 37.3 + - + +
102A ALA* 1.3 71.9 - - - +
104A GLN* 1.3 56.9 + - - +
106A PHE* 3.3 1.9 + - - +
107A ASN* 2.8 37.6 + - - +
176A ALA* 3.3 29.6 - - + +
178A CYS* 4.6 4.9 - - + -
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Residues in contact with GLN 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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66A TYR* 3.1 51.0 + - + +
100A ASN 3.0 22.0 + - - +
103A ALA* 1.3 73.2 - - - +
105A HIS* 1.3 62.0 + - - +
107A ASN* 3.2 15.5 + - - +
108A HIS* 2.7 53.8 + - - +
156A TRP* 3.0 23.8 + - - +
176A ALA* 3.4 17.8 - - + -
193A TRP* 3.3 26.1 - - - +
195A HIS* 5.2 0.2 - - - -
152B PHE* 3.9 4.3 - - + -
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Residues in contact with HIS 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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29A LEU* 3.7 16.8 - - + +
30A ARG 4.9 0.8 + - - -
33A ALA* 3.7 20.2 - - + +
34A GLU 3.4 25.3 + - - -
36A PRO* 4.4 0.2 - - + -
63A HIS* 3.0 31.2 + + - +
66A TYR* 4.4 7.3 - - + +
67A VAL* 3.7 14.2 - - + +
70A LEU* 4.2 5.2 - - + -
82A ILE* 3.6 33.7 - - + +
101A GLN 2.9 18.9 + - - +
102A ALA* 3.6 6.1 - - - +
104A GLN* 1.3 75.8 - - - +
106A PHE* 1.3 61.4 + - - +
109A SER* 2.8 47.0 + - - -
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Residues in contact with PHE 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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25A THR* 3.7 25.1 - - + -
26A LEU* 3.8 22.9 - - + -
29A LEU* 3.8 15.3 - - + -
82A ILE* 4.1 5.8 - - + +
83A GLU* 3.4 39.3 - - + -
86A ILE* 3.6 13.5 - - + -
102A ALA 2.9 14.1 + - - +
103A ALA 3.6 5.6 - - - +
105A HIS* 1.3 77.2 - - - +
107A ASN* 1.3 72.5 + - - +
109A SER* 3.8 1.0 - - - -
110A PHE* 2.9 39.5 + - + +
158A TRP* 4.4 11.4 - + - -
178A CYS* 3.6 20.2 - - - -
180A LEU* 4.3 4.0 - - + -
186A PRO* 4.5 7.2 - - + -
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Residues in contact with ASN 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 2.8 23.7 + - - +
104A GLN* 3.2 17.4 + - - +
105A HIS 3.4 0.2 - - - -
106A PHE* 1.3 84.4 - - - +
108A HIS* 1.3 57.8 + - - +
110A PHE* 3.5 2.2 + - - +
111A PHE* 2.9 28.4 + - - +
156A TRP* 3.4 36.1 - - + +
158A TRP* 3.2 29.0 - - + -
176A ALA 3.1 26.1 + - - -
177A GLY 3.7 4.6 + - - -
178A CYS* 3.6 7.6 - - - -
189A THR* 4.3 2.1 - - - +
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Residues in contact with HIS 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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58A HIS* 3.1 40.7 + + - -
62A HIS* 5.0 0.8 - - - +
63A HIS* 3.5 28.7 - + + +
66A TYR* 3.6 19.8 - + - -
104A GLN* 2.7 47.6 + - - +
107A ASN* 1.3 76.0 - - - +
109A SER* 1.3 65.2 + - - +
111A PHE* 3.2 5.9 + + - +
112A TRP* 3.0 38.1 + + - +
156A TRP* 3.5 22.8 - + - -
191A ASP* 3.4 9.3 + - - -
195A HIS* 3.7 6.3 + - - -
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Residues in contact with SER 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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26A LEU* 4.1 6.1 - - - -
29A LEU* 3.6 23.0 - - - +
36A PRO* 3.6 12.5 - - - +
63A HIS* 3.3 17.3 - - - -
105A HIS* 2.8 37.4 + - - -
106A PHE 3.8 3.4 - - - -
108A HIS* 1.3 75.2 - - - +
110A PHE* 1.3 61.6 + - - +
112A TRP* 3.4 8.1 + - - +
113A LYS* 3.4 27.0 + - - +
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Residues in contact with PHE 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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25A THR* 3.5 31.6 - - + -
26A LEU* 3.8 14.0 - - + +
106A PHE* 2.9 28.3 + + + +
107A ASN* 3.7 3.1 - - - +
109A SER* 1.3 74.1 - - - +
111A PHE* 1.3 64.4 + - - +
113A LYS* 3.2 14.6 + - - +
114A CYS* 3.2 33.1 + - - -
158A TRP* 3.8 9.6 - + - -
186A PRO* 3.7 19.1 - - + -
187A ILE* 3.5 25.6 - - - -
188A PHE 3.7 17.5 - - - -
189A THR* 3.7 15.3 - - + -
220A PHE* 3.6 24.7 - + - -
224A MET* 4.3 3.4 - - + -
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Residues in contact with PHE 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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50A MET* 3.9 14.4 - - + -
58A HIS* 4.0 14.4 - + - -
107A ASN 2.9 19.1 + - - +
108A HIS* 3.3 10.1 - + - +
110A PHE* 1.3 72.8 - - - +
112A TRP* 1.3 85.0 + + - +
114A CYS* 3.0 20.4 + - + +
115A LEU* 3.4 39.7 - - + +
156A TRP* 4.0 10.1 - + + -
189A THR* 3.5 31.4 - - + -
190A ALA* 3.8 3.4 - - - -
191A ASP* 3.6 30.5 - - + -
196A ALA* 5.1 0.2 - - + -
208A TYR* 3.5 20.4 - - - -
212A LEU* 4.6 6.3 - - + -
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Residues in contact with TRP 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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36A PRO* 3.9 11.2 - - + -
38A LEU* 3.5 32.3 - - + -
39A GLY 5.8 0.3 + - - -
40A PHE* 4.0 8.9 - + + -
46A ILE* 4.7 4.7 - - + -
50A MET* 4.8 3.1 - - - -
55A LEU* 3.6 29.4 - - + -
58A HIS* 3.5 39.0 - + + -
59A TYR* 3.7 28.0 - + + -
63A HIS* 2.9 30.1 + + - -
108A HIS* 3.0 33.4 + + + +
109A SER* 4.0 3.4 - - - +
110A PHE 3.3 0.4 - - - -
111A PHE* 1.3 96.3 - + - +
113A LYS* 1.3 62.3 + - + +
115A LEU* 3.2 34.3 + - + +
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Residues in contact with LYS 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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26A LEU* 3.8 27.4 - - + -
36A PRO* 6.6 0.4 - - + -
109A SER* 3.4 11.6 + - - +
110A PHE 3.2 9.5 + - - +
112A TRP* 1.3 79.0 - - + +
114A CYS* 1.3 58.6 + - - +
115A LEU 3.2 2.7 + - - +
217A ASP* 4.0 7.8 - - - +
220A PHE* 3.3 56.7 - - + +
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Residues in contact with CYS 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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110A PHE* 3.2 41.6 + - - -
111A PHE* 3.0 14.9 + - + +
113A LYS* 1.3 76.4 - - - +
115A LEU* 1.3 57.9 + - + +
187A ILE 4.2 1.1 - - - -
188A PHE* 3.7 35.7 - - + -
189A THR 3.9 5.6 - - - +
216A VAL* 3.5 10.7 - - - +
217A ASP* 2.7 30.6 + - - -
220A PHE* 4.0 15.9 - - - -
221A VAL* 4.7 0.9 - - - -
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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