Contacts of the helix formed by residues 87 - 100 (chain A) in PDB entry 6BSL
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 LYS 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A VAL* 4.1 1.6 - - - -
85A CYS* 3.6 1.8 - - - +
86A ASP* 1.3 87.2 - - - +
88A PHE* 1.3 66.9 - - - +
89A GLY 3.3 3.4 - - - +
90A ILE* 3.0 26.1 + - + +
91A VAL* 3.0 10.6 + - - +
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Residues in contact with PHE 88 (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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30A VAL* 3.5 24.1 - - + +
33A GLN* 3.6 36.6 - - + +
34A ALA* 3.6 18.2 - - - -
37A HIS* 3.6 32.3 - + + -
87A LYS* 1.3 70.9 - - - +
89A GLY* 1.3 60.1 + - - +
91A VAL* 3.1 5.7 + - - +
92A VAL* 2.9 40.4 + - + +
182A ARG 5.5 0.2 - - - -
183A THR 3.4 25.4 - - - -
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Residues in contact with GLY 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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87A LYS* 3.3 3.0 - - - +
88A PHE* 1.3 89.5 - - - +
90A ILE* 1.3 57.0 + - - +
92A VAL* 3.5 7.0 + - - +
93A HIS* 3.0 26.0 + - - +
149A ILE* 3.8 8.8 - - - +
182A ARG* 3.2 34.0 + - - -
183A THR 4.8 0.7 - - - -
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Residues in contact with ILE 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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84A ASN 5.6 0.4 - - - +
85A CYS* 3.5 41.7 - - + +
87A LYS* 3.0 21.7 + - + +
89A GLY* 1.3 73.4 - - - +
91A VAL* 1.3 61.7 + - - +
93A HIS* 3.2 9.7 + - + +
94A GLU* 2.9 39.9 + - + +
182A ARG* 3.8 31.0 - - + +
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Residues in contact with VAL 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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30A VAL* 4.4 2.9 - - + -
31A PHE* 3.8 34.1 - - + -
34A ALA* 3.5 21.1 - - + -
58A PHE* 4.0 13.2 - - + -
79A ILE* 4.7 2.9 - - + -
81A ILE* 3.9 13.9 - - + -
86A ASP* 3.7 16.8 - - - +
87A LYS 3.0 14.6 + - - +
88A PHE 3.1 6.5 + - - +
90A ILE* 1.3 76.4 - - - +
92A VAL* 1.3 56.1 + - - +
94A GLU* 3.2 6.0 + - - +
95A LEU* 2.8 38.3 + - + +
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Residues in contact with VAL 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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34A ALA* 3.8 17.5 - - + +
37A HIS* 3.9 16.6 - - + +
38A TRP* 3.0 29.6 + - - +
88A PHE* 2.9 48.1 + - + +
89A GLY* 3.6 9.6 - - - +
90A ILE 3.3 0.2 - - - -
91A VAL* 1.3 76.0 - - - +
93A HIS* 1.3 56.5 + - - +
95A LEU* 3.3 1.9 + - - -
96A GLY* 3.0 22.7 + - - -
149A ILE* 4.0 13.4 - - + +
184A ARG* 5.0 0.4 - - - -
185A LEU* 3.8 20.6 - - + +
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Residues in contact with HIS 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 GLY 3.0 14.2 + - - +
90A ILE* 3.2 12.3 + - + +
92A VAL* 1.3 75.7 - - - +
94A GLU* 1.3 61.6 + - + +
96A GLY* 2.9 21.5 + - - -
97A HIS* 3.3 6.1 + - - -
103A HIS* 3.4 18.6 - + - -
149A ILE* 2.7 32.5 + - + +
150A MET* 3.3 23.4 - - + +
152A TYR* 5.7 0.9 - + - -
182A ARG* 3.3 28.8 + - - +
302A ZN 2.1 36.4 - - - -
304A EVV 3.0 12.2 + - - -
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Residues in contact with GLU 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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64A GLY 5.5 1.6 + - - +
67A SER* 3.3 17.4 + - - +
79A ILE* 3.6 18.8 - - + +
80A SER 2.5 30.1 - - - +
81A ILE* 3.2 14.9 - - - +
85A CYS* 4.6 7.6 - - - +
90A ILE* 2.9 31.9 + - + +
91A VAL* 3.8 3.1 - - - +
93A HIS* 1.3 79.1 - - + +
95A LEU* 1.3 58.1 + - - +
97A HIS* 3.1 23.5 + - - +
98A VAL* 3.1 13.9 + - - +
304A EVV 3.4 32.2 - - - +
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Residues in contact with LEU 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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34A ALA* 3.6 17.3 - - + +
35A MET* 3.6 40.6 - - + +
38A TRP* 3.5 22.0 - - + +
46A PHE* 3.9 25.1 - - + -
56A ILE* 4.1 13.0 - - + -
58A PHE* 4.2 3.4 - - + -
79A ILE* 3.7 18.8 - - + -
91A VAL* 2.8 26.5 + - + +
94A GLU* 1.3 72.9 - - - +
96A GLY* 1.3 59.8 + - - +
98A VAL* 3.1 8.2 + - + +
99A VAL* 3.0 32.4 + - - +
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Residues in contact with GLY 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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38A TRP* 3.5 22.8 - - - -
92A VAL 3.0 7.5 + - - -
93A HIS 2.9 11.3 + - - -
95A LEU* 1.3 72.1 - - - +
97A HIS* 1.3 61.6 + - - +
99A VAL* 3.3 6.6 - - - +
100A GLY 3.3 6.1 + - - -
101A PHE* 2.9 27.9 + - - +
150A MET* 3.8 13.5 - - - -
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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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67A SER* 4.2 8.7 - - - +
68A TYR 3.6 12.1 - - - +
69A VAL* 3.2 13.3 - - + +
70A GLY 2.8 19.8 + - - -
93A HIS* 3.3 9.3 + + - -
94A GLU* 3.1 13.8 + - - +
96A GLY* 1.3 73.7 - - - +
98A VAL* 1.3 65.9 + - - +
100A GLY* 3.0 7.4 + - - -
101A PHE 2.8 23.3 + - - -
102A TRP* 4.3 1.8 - + - -
103A HIS* 3.3 20.6 - + - -
150A MET* 3.4 13.1 - - + +
302A ZN 2.1 37.3 - - - -
304A EVV 3.1 37.4 + - - -
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Residues in contact with VAL 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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10A TRP* 2.9 25.9 + - + +
15A ILE* 3.9 23.1 - - + -
46A PHE* 4.6 3.6 - - + -
56A ILE* 3.6 34.5 - - + -
67A SER* 5.8 0.9 - - - -
68A TYR 3.7 11.6 + - - +
70A GLY* 3.1 15.5 - - - -
77A GLN* 4.7 2.0 - - - +
78A ALA 5.4 1.6 - - - +
79A ILE* 4.1 29.4 - - + -
94A GLU 3.1 11.6 + - - +
95A LEU* 3.1 15.5 + - + +
97A HIS* 1.3 77.5 - - + +
99A VAL* 1.3 57.3 + - - +
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Residues in contact with VAL 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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3A THR* 5.4 0.2 - - - +
8A ARG 4.5 3.1 - - - +
9A VAL* 5.1 0.9 - - - -
10A TRP* 4.4 2.0 - - - -
15A ILE* 3.8 22.0 - - + -
38A TRP* 3.7 26.2 - - + -
44A VAL* 4.3 13.7 - - + -
46A PHE* 4.5 7.6 - - + -
70A GLY* 4.3 0.9 - - - -
95A LEU 3.0 18.0 + - - +
96A GLY 3.3 14.8 - - - +
98A VAL* 1.3 76.6 - - + +
100A GLY* 1.3 55.9 + - - +
101A PHE* 3.5 25.1 - - + -
193A ALA* 5.4 0.4 - - + -
196A LEU* 3.9 5.1 - - - +
197A TYR* 2.7 42.5 + - + +
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Residues in contact with GLY 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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2A ALA* 3.7 1.7 - - - +
3A THR* 2.9 42.1 + - - +
69A VAL* 3.7 6.5 - - - +
70A GLY* 3.7 16.2 - - - -
96A GLY 3.3 0.6 + - - -
97A HIS 3.0 9.8 + - - -
99A VAL* 1.3 79.8 - - - +
101A PHE* 1.3 65.1 + - - +
196A LEU* 4.6 3.5 - - - +
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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