Contacts of the helix formed by residues 71 - 82 (chain A) in PDB entry 2KBS
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 ASP 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A ILE* 3.3 0.9 - - - +
69A ASN 3.6 2.4 + - - -
70A LEU* 1.3 83.6 - - - +
72A HIS* 1.3 71.2 + - - +
73A LYS* 4.1 13.5 + - - +
74A GLU* 3.2 20.5 + - + +
75A ALA 3.0 17.7 + - - -
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Residues in contact with HIS 72 (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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27A ILE* 3.5 36.5 + - + +
28A SER* 4.1 3.0 - - - -
29A SER* 3.2 34.7 + - - +
37A ILE* 3.7 12.3 - - + +
70A LEU 3.8 0.8 + - - -
71A ASP* 1.3 77.0 - - - +
73A LYS* 1.3 65.6 + - + +
75A ALA* 3.0 12.6 + - - +
76A VAL* 3.2 12.8 + - + +
114B GLU* 3.7 27.0 + - + +
115B ILE 4.2 0.2 - - - -
116B THR* 3.0 30.7 + - - -
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Residues in contact with LYS 73 (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 ASP* 3.4 11.8 + - - +
72A HIS* 1.3 79.2 - - + +
74A GLU* 1.3 52.3 + - - +
76A VAL* 3.2 8.0 + - - +
77A ASN* 2.7 49.9 + - - +
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Residues in contact with GLU 74 (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* 4.9 2.1 - - - +
70A LEU* 3.3 30.1 - - + +
71A ASP* 3.2 23.6 + - + +
73A LYS* 1.3 79.8 - - - +
75A ALA* 1.3 61.3 + - - +
77A ASN* 4.2 6.2 - - - +
78A VAL* 3.0 43.6 + - - +
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Residues in contact with ALA 75 (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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27A ILE* 4.2 6.7 - - + -
37A ILE* 3.2 41.3 - - + -
67A PHE* 3.3 15.7 - - + -
70A LEU* 3.0 17.7 - - + +
72A HIS 3.0 5.9 + - - +
74A GLU* 1.3 77.4 - - - +
76A VAL* 1.3 61.1 + - - +
78A VAL* 3.1 0.5 - - - +
79A LEU* 3.1 32.9 + - + +
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Residues in contact with VAL 76 (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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27A ILE* 3.2 27.8 - - + -
72A HIS* 3.2 14.9 + - - +
73A LYS* 3.8 7.2 - - - +
75A ALA* 1.3 73.2 - - - +
77A ASN* 1.3 61.4 + - - +
79A LEU* 4.4 3.4 - - - -
80A LYS* 2.8 48.5 + - + +
116B THR* 3.5 29.4 - - + +
118B LEU* 3.6 18.4 - - + -
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Residues in contact with ASN 77 (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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73A LYS* 2.7 32.7 + - - +
74A GLU* 3.6 10.8 - - - +
76A VAL* 1.3 74.1 - - - +
78A VAL* 1.3 54.0 + - + +
80A LYS* 3.0 5.8 + - - +
81A SER* 2.7 39.1 + - - -
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Residues in contact with VAL 78 (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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62A VAL* 4.3 7.0 - - + +
65A VAL* 5.1 16.2 - - + -
67A PHE* 3.5 18.2 - - + -
74A GLU* 3.0 34.7 + - - +
75A ALA 3.1 8.7 - - - +
77A ASN* 1.3 76.6 + - + +
79A LEU* 1.3 77.1 + - + +
81A SER* 3.6 7.3 - - - -
82A SER* 3.2 14.2 + - - -
85A LEU* 3.2 17.0 - - + +
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Residues in contact with LEU 79 (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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15A ILE* 5.7 2.7 - - + -
23A LEU* 5.5 8.5 - - + -
27A ILE* 5.8 0.2 - - + -
59A ILE* 5.5 7.0 - - + -
62A VAL* 3.4 34.3 - - + -
67A PHE* 4.0 4.7 - - + -
75A ALA 3.1 25.0 + - - +
76A VAL* 3.8 6.1 - - - +
78A VAL* 1.3 86.6 - - + +
80A LYS* 1.3 62.5 + - + +
82A SER 3.0 18.9 - - - +
83A ARG* 4.8 1.9 - - - +
85A LEU* 3.7 26.7 - - + +
87A ILE* 4.2 18.6 - - + -
118B LEU* 4.5 22.4 - - + -
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Residues in contact with LYS 80 (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 VAL* 2.8 36.9 + - + +
77A ASN* 3.5 5.6 - - - +
79A LEU* 1.3 81.6 + - - +
81A SER* 1.3 66.4 + - - +
82A SER 4.5 1.7 - - - -
83A ARG* 4.8 1.4 + - - -
117B GLU 3.9 7.3 + - - -
118B LEU* 3.3 53.5 + - + +
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Residues in contact with SER 81 (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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77A ASN* 2.7 22.1 + - - -
78A VAL* 3.3 9.2 + - - -
80A LYS* 1.3 75.8 - - - +
82A SER* 1.3 62.0 + - - +
83A ARG 3.8 1.7 + - - -
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Residues in contact with SER 82 (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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63A ASN* 4.6 9.4 + - - -
78A VAL 3.2 3.9 + - - -
79A LEU 3.0 11.6 - - - +
80A LYS 4.5 0.4 - - - -
81A SER* 1.3 79.9 - - - +
83A ARG* 1.3 60.8 + - - +
84A SER 4.3 8.9 + - - -
85A LEU* 3.0 43.2 - - - +
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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