Contacts of the helix formed by residues 84 - 96 (chain A) in PDB entry 2KSB
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 84 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A PHE* 6.1 3.8 - + - -
80A SER* 2.6 44.3 + - - +
83A ALA* 1.4 88.0 - - + +
85A ASN* 1.4 68.1 + - + +
87A VAL* 4.0 0.7 - - - +
88A VAL* 3.5 24.3 + - - +
108A HIS* 4.9 2.1 - - - -
111A PHE* 5.0 30.1 - + + -
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Residues in contact with ASN 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TYR* 3.1 18.4 + - - -
80A SER 3.3 1.2 + - - -
81A MET* 2.7 58.5 + - - +
84A PHE* 1.4 78.1 - - - +
86A THR* 1.3 83.4 + - - +
87A VAL 3.2 0.3 + - - -
88A VAL* 3.3 5.2 + - - +
89A ASN* 3.1 31.4 + - - +
108A HIS* 5.6 3.4 - - - -
112A PRO* 3.0 45.0 - - + +
115A ALA* 5.0 2.3 - - - +
295A MET* 3.8 4.7 - - - -
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Residues in contact with THR 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TYR* 2.8 55.5 + - - -
42A ILE* 4.8 3.0 - - - +
43A VAL* 3.1 31.6 + - + +
81A MET* 2.7 17.2 + - - -
82A ALA* 2.7 34.5 - - - +
85A ASN* 1.3 74.4 - - - +
87A VAL* 1.3 68.8 + - + +
89A ASN 3.2 0.2 + - - -
90A PHE* 2.8 23.1 + - - +
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Residues in contact with VAL 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A VAL* 5.4 6.7 - - + -
82A ALA 3.9 6.5 - - - +
83A ALA* 2.7 31.0 - - - +
84A PHE 4.0 3.1 - - - +
85A ASN 3.2 0.8 - - - -
86A THR* 1.3 85.3 - - + +
88A VAL* 1.3 65.4 + - + +
90A PHE* 3.2 8.4 + - - +
91A THR* 3.1 27.2 + - - +
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Residues in contact with VAL 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PHE 3.5 13.2 - - - +
85A ASN 3.3 4.4 + - - +
87A VAL* 1.3 76.7 - - + +
89A ASN* 1.3 69.0 + - - +
91A THR* 3.1 8.1 + - - -
92A TYR* 3.0 22.0 + - - +
98A TRP* 3.5 17.5 - - + -
100A TYR* 4.0 14.1 - - + +
108A HIS* 2.8 60.1 - - + +
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Residues in contact with ASN 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TYR* 2.9 38.8 + - + -
85A ASN* 3.1 21.8 + - - +
88A VAL* 1.3 82.9 - - - +
90A PHE* 1.3 59.5 + - - +
92A TYR* 3.6 5.9 - - - -
93A ALA* 3.1 22.3 + - - +
108A HIS* 5.2 8.1 - - - +
112A PRO* 5.4 2.1 - - - +
178A VAL* 3.5 23.0 + - - +
179A VAL* 4.1 14.4 - - - +
180A CYS 5.2 0.4 - - - +
292A TRP* 4.0 9.7 - - + -
295A MET* 3.3 18.1 - - - +
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Residues in contact with PHE 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ALA* 2.8 50.5 - - + -
37A ALA* 4.9 0.7 - - - -
39A TYR* 3.7 10.5 - - + -
40A THR* 4.0 23.6 - - + +
43A VAL* 5.7 3.4 - - + -
86A THR 2.8 14.2 + - - +
87A VAL* 3.4 11.4 - - - +
88A VAL 3.1 0.2 - - - -
89A ASN* 1.3 75.6 - - - +
91A THR* 1.3 71.1 + - - +
93A ALA* 3.0 13.0 + - - +
94A VAL* 3.1 31.7 + - + +
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Residues in contact with THR 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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87A VAL* 3.1 22.2 + - - +
88A VAL* 3.1 7.7 + - - -
90A PHE* 1.3 81.8 - - - +
92A TYR* 1.3 66.3 + - - +
94A VAL* 3.4 4.8 + - - +
95A HIS* 2.8 55.2 + - + +
99A TYR* 5.8 0.4 - - + -
100A TYR* 3.3 33.9 + - + +
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Residues in contact with TYR 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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23A ASN* 5.0 0.9 - - - +
27A GLN* 4.5 2.8 + - - -
32A ILE* 4.9 3.1 - - - +
88A VAL 3.0 6.3 + - - +
89A ASN 3.6 5.8 - - - +
91A THR* 1.3 81.8 - - - +
93A ALA* 1.3 68.4 + - - +
95A HIS* 2.8 4.2 + - - -
96A ASN* 2.6 48.4 + - - -
97A GLU* 2.9 49.3 + - - +
98A TRP* 4.5 2.9 - - + -
99A TYR* 6.3 0.2 - - - -
100A TYR* 5.1 3.1 - - - -
176A SER* 2.6 23.0 + - - -
177A ARG* 2.9 41.3 + - - -
178A VAL* 2.8 56.3 - - + -
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Residues in contact with ALA 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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32A ILE* 2.7 29.0 - - - +
35A TRP 4.4 3.1 - - - -
36A ALA* 3.8 29.2 - - + +
89A ASN 3.1 13.3 + - - +
90A PHE* 3.0 6.9 + - - +
92A TYR* 1.3 97.4 - - + +
94A VAL* 1.3 62.6 + - - +
96A ASN* 3.1 8.7 + - - +
177A ARG* 4.5 6.7 - - - +
292A TRP* 4.6 1.3 - - + -
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Residues in contact with VAL 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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32A ILE* 4.0 4.5 - - + +
33A VAL* 4.6 15.3 - - + -
36A ALA* 3.0 32.5 - - + -
90A PHE* 3.1 35.4 + - + +
91A THR* 3.6 9.0 - - + +
93A ALA* 1.3 80.9 - - - +
95A HIS* 1.3 65.1 + - + +
96A ASN* 3.8 8.1 + - - +
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Residues in contact with HIS 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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22A PRO* 4.0 12.1 - - - +
91A THR* 2.8 49.4 + - + +
92A TYR* 2.8 7.4 + - - +
94A VAL* 1.3 82.2 - - + +
96A ASN* 1.3 69.0 + - - +
97A GLU 3.2 15.2 + - - +
99A TYR* 4.8 24.2 - + + +
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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
----------------------------------------------------------
22A PRO* 2.5 46.0 - - + +
23A ASN* 3.3 2.4 - - - +
24A GLN* 3.8 23.5 + - - +
29A ALA* 5.4 5.5 - - - +
32A ILE* 2.7 47.8 - - + +
92A TYR* 2.6 29.0 + - - -
93A ALA 3.1 2.2 + - - -
94A VAL 3.8 5.0 + - - +
95A HIS* 1.3 77.0 + - - +
97A GLU* 1.4 66.7 + - - +
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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
------------------------------------------------------------
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