Contacts of the helix formed by residues 88 - 101 (chain A) in PDB entry 5W4A
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 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A VAL* 3.8 37.2 - - + -
60A ILE* 4.2 35.0 - - + -
61A VAL* 4.5 7.2 - - + -
81A LEU* 3.6 44.5 - - + +
84A LEU* 3.4 42.4 - - + -
85A GLY 2.9 4.5 + - - -
87A ASP* 1.3 93.5 - - + +
89A LEU* 1.3 56.8 + - - +
90A THR 3.4 2.5 - - - -
91A GLU* 3.3 11.4 + - + +
92A PHE* 3.0 26.1 + - - +
178A ILE* 5.6 1.6 - - + -
179A LEU* 5.6 3.1 - - + -
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Residues in contact with LEU 89 (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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82A LEU* 4.5 13.2 - - + -
85A GLY 3.7 2.5 + - - +
86A PRO* 3.1 26.1 + - + +
88A PHE* 1.3 76.0 - - - +
90A THR* 1.3 67.2 + - - +
92A PHE* 3.1 24.8 + - + +
93A LYS* 2.9 49.9 + - - +
111A LEU* 5.2 10.5 - - + +
112A ALA* 4.8 7.2 - - + +
116A GLU* 6.4 2.0 - - + -
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Residues in contact with THR 90 (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 PRO 4.7 1.2 + - - -
87A ASP 5.0 3.5 + - - -
88A PHE* 3.4 0.6 - - - +
89A LEU* 1.3 77.0 - - - +
91A GLU* 1.3 63.0 + - - +
93A LYS* 3.3 11.9 + - + +
94A LYS* 3.0 45.6 + - + +
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Residues in contact with GLU 91 (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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57A VAL* 6.4 0.7 - - + -
61A VAL* 3.9 31.4 - - + +
65A PHE* 4.7 0.7 - - + -
81A LEU* 3.8 18.8 - - + -
87A ASP 5.7 0.4 + - - -
88A PHE* 3.3 14.8 + - + +
89A LEU 3.2 0.4 - - - -
90A THR* 1.3 77.9 - - - +
92A PHE* 1.3 62.3 + - - +
94A LYS* 3.2 28.4 + - - +
95A ARG* 2.8 66.9 + - - +
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Residues in contact with PHE 92 (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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78A MSE 3.6 41.0 - - + +
81A LEU* 3.6 15.3 - - + +
82A LEU* 3.5 36.6 - - + -
88A PHE 3.0 13.8 + - - +
89A LEU* 3.1 23.5 + - + +
91A GLU* 1.3 76.3 - - - +
93A LYS* 1.3 68.6 + - + +
95A ARG* 3.3 2.8 + - - -
96A ASN* 2.9 29.1 + - + +
106A HIS* 3.7 35.4 - + + -
108A LEU 4.8 6.7 - - - -
109A SER* 4.8 4.0 - - - -
111A LEU* 5.8 0.9 - - + -
112A ALA* 4.1 18.6 - - + -
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Residues in contact with LYS 93 (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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89A LEU* 2.9 44.1 + - + +
90A THR* 3.7 9.4 - - + +
92A PHE* 1.3 79.6 - - + +
94A LYS* 1.3 58.6 + - + +
96A ASN* 3.3 4.6 + - - +
97A GLN* 2.9 30.7 + - - +
112A ALA* 3.8 43.6 + - + +
116A GLU* 5.9 0.8 + - - -
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Residues in contact with LYS 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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90A THR* 3.0 42.1 + - + +
91A GLU* 3.2 28.9 + - - +
93A LYS* 1.3 78.0 - - + +
95A ARG* 1.3 64.4 + - + +
97A GLN* 3.3 14.9 + - - +
98A ASP* 3.1 22.3 + - - +
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Residues in contact with ARG 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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61A VAL* 3.8 10.9 - - - +
62A GLN* 5.6 2.4 + - - +
65A PHE* 3.5 63.5 + - + +
69A SER* 6.3 0.4 - - - -
74A ILE* 4.5 13.9 - - + +
78A MSE 3.8 21.5 - - + -
81A LEU* 4.6 0.2 - - + -
91A GLU* 2.8 47.7 + - - +
92A PHE 3.7 3.8 - - - +
94A LYS* 1.3 76.3 - - - +
96A ASN* 1.3 63.5 + - - +
98A ASP* 3.3 8.7 + - - +
99A LEU* 3.2 24.9 + - - +
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Residues in contact with ASN 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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78A MSE 3.4 15.1 - - + +
92A PHE* 2.9 24.3 + - + +
93A LYS* 3.7 7.0 - - - +
95A ARG* 1.3 73.0 - - - +
97A GLN* 1.3 67.4 + - - +
99A LEU* 3.2 14.7 + - - +
100A ALA* 3.3 11.4 + - - +
104A LEU 4.5 1.2 - - - +
105A THR* 3.2 13.3 + - - -
106A HIS* 2.9 26.4 + - - -
109A SER* 2.8 31.0 + - - +
112A ALA* 5.5 3.8 - - - +
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Residues in contact with GLN 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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93A LYS 2.9 16.7 + - - +
94A LYS* 3.7 13.2 - - - +
96A ASN* 1.3 75.1 - - - +
98A ASP* 1.3 63.6 + - - +
100A ALA* 3.2 21.1 + - + +
101A ARG* 4.2 6.4 + - - +
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Residues in contact with ASP 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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74A ILE* 5.2 6.8 - - - +
94A LYS 3.1 14.0 + - - +
95A ARG* 3.7 11.0 - - - +
96A ASN 3.2 0.2 - - - -
97A GLN* 1.3 79.8 - - - +
99A LEU* 1.3 68.7 + - - +
100A ALA 3.4 0.5 + - - -
101A ARG* 2.4 49.1 + - - +
102A PHE* 3.6 14.6 - - - -
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Residues in contact with LEU 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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71A SER* 4.7 7.2 - - - -
74A ILE* 4.2 25.1 - - + -
75A LEU* 3.8 31.4 - - + -
78A MSE 3.8 19.3 - - - -
95A ARG 3.2 14.6 + - - +
96A ASN* 3.2 15.3 + - - +
98A ASP* 1.3 83.0 - - - +
100A ALA* 1.3 65.0 + - - +
102A PHE* 2.9 22.7 + - + +
104A LEU* 3.2 45.4 + - + +
105A THR* 4.5 4.9 - - - -
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Residues in contact with ALA 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 ASN 3.3 7.5 + - - +
97A GLN* 3.2 16.5 + - + +
99A LEU* 1.3 78.1 - - - +
101A ARG* 1.3 64.2 + - + +
103A ASN* 2.9 18.5 + - - +
104A LEU 3.6 10.3 - - - +
105A THR* 6.3 0.4 - - - -
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Residues in contact with ARG 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 GLN 4.5 4.7 - - - +
98A ASP* 2.4 49.7 + - - +
99A LEU 3.1 0.6 + - - -
100A ALA* 1.3 78.6 - - + +
102A PHE* 1.3 91.7 + - + +
103A ASN* 3.3 5.1 + - - +
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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