Contacts of the helix formed by residues 83 - 95 (chain A) in PDB entry 2KN4
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 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A ARG 3.6 7.4 + - - -
82A THR* 1.3 75.3 - - - +
84A PRO* 1.3 66.3 - - - +
85A ASP* 4.4 7.6 - - - -
86A THR* 2.8 41.8 + - - -
102A ILE* 3.1 9.1 - - - +
104A ARG* 4.6 5.2 + - - +
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Residues in contact with PRO 84 (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 THR 4.4 1.6 - - - +
83A SER* 1.3 86.4 - - - +
85A ASP* 1.3 62.4 + - - +
86A THR 3.1 0.9 + - - -
87A LEU 3.3 2.8 + - - -
88A ARG 3.2 17.0 + - - -
100A VAL* 3.2 26.6 - - + +
102A ILE* 3.2 41.1 - - + +
104A ARG* 5.0 6.7 - - - +
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Residues in contact with ASP 85 (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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83A SER* 3.2 6.7 - - - -
84A PRO* 1.3 80.1 - - - +
86A THR* 1.3 58.2 + - - +
88A ARG* 3.6 11.4 - - - +
89A ARG* 2.9 48.3 + - - +
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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
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82A THR* 3.5 20.8 - - + -
83A SER* 2.8 29.8 + - - -
85A ASP* 1.3 85.1 + - - +
87A LEU* 1.3 65.1 + - + +
89A ARG* 3.3 22.5 + - - +
90A VAL* 3.0 27.0 + - + +
137A LEU* 3.8 27.7 - - + +
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Residues in contact with LEU 87 (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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75A VAL* 3.5 33.7 - - + -
78A LEU* 4.2 2.7 - - + -
82A THR* 4.0 11.9 - - + -
83A SER 3.6 0.6 + - - -
84A PRO 3.3 3.1 + - - +
86A THR* 1.3 81.3 - - + +
88A ARG* 1.3 62.4 + - - +
90A VAL* 3.1 4.0 + - + -
91A PHE* 2.8 56.3 + - + -
100A VAL* 4.4 1.3 - - + -
102A ILE* 3.4 29.8 - - + -
115A ALA* 3.6 10.1 - - + -
117A VAL* 4.2 9.9 - - + -
132A MET* 4.9 4.0 - - + -
137A LEU* 4.8 3.1 - - + -
142A LEU* 4.5 24.7 - - + -
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Residues in contact with ARG 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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84A PRO 3.2 16.6 + - - +
85A ASP* 3.6 11.4 - - - +
86A THR 3.3 0.2 - - - -
87A LEU* 1.3 78.3 - - - +
89A ARG* 1.3 61.6 + - - +
91A PHE* 4.9 1.3 - - - -
92A GLU* 3.1 35.8 + - - +
97A VAL* 3.9 12.5 + - + +
98A GLY 3.0 27.2 + - - -
99A ASP* 4.1 19.3 + - - +
100A VAL* 3.6 30.0 - - + +
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Residues in contact with ARG 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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85A ASP* 2.9 39.6 + - - +
86A THR* 3.6 24.6 + - - +
87A LEU 3.2 0.2 - - - -
88A ARG* 1.3 76.9 - - - +
90A VAL* 1.3 68.2 + - - +
92A GLU* 3.1 29.3 - - - +
93A LYS* 4.3 3.6 + - - +
137A LEU 5.6 3.6 + - - -
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Residues in contact with VAL 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 THR* 3.0 24.7 - - + +
87A LEU* 3.1 8.4 + - + +
89A ARG* 1.3 88.9 - - - +
91A PHE* 1.3 65.3 + - - +
93A LYS* 3.0 24.9 + - + +
94A TYR* 3.3 17.6 - - + +
132A MET* 3.5 30.1 - - + -
135A ALA* 5.8 1.8 - - + -
137A LEU* 5.4 8.5 - - + -
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Residues in contact with PHE 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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73A LEU* 4.6 0.2 - - + -
75A VAL* 3.4 23.8 - - + -
87A LEU* 2.8 52.0 + - + +
88A ARG* 4.4 1.6 - - - +
90A VAL* 1.3 74.1 - - - +
92A GLU* 1.3 56.5 + - - +
93A LYS 3.0 0.2 - - - -
94A TYR* 2.9 24.0 + - - +
95A GLY 3.1 9.9 + - - -
97A VAL* 4.6 4.3 - - + -
117A VAL* 3.6 36.3 - - + -
119A PHE* 3.3 30.0 - + + -
128A ALA* 3.8 11.0 - - + -
132A MET* 3.5 36.3 - - + -
144A VAL* 3.7 24.2 - - + -
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Residues in contact with GLU 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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88A ARG* 3.1 23.7 + - - +
89A ARG* 3.1 30.4 - - - +
91A PHE* 1.3 75.1 - - - +
93A LYS* 1.3 60.3 + - + +
95A GLY 3.2 20.4 - - - +
96A ARG* 5.1 0.9 - - - -
97A VAL* 3.4 16.8 - - + +
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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 ARG 4.7 3.8 - - - +
90A VAL* 3.0 15.1 + - + +
91A PHE 3.0 1.0 + - - -
92A GLU* 1.3 81.9 - - + +
94A TYR* 1.3 80.3 + - + +
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Residues in contact with TYR 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 VAL* 3.3 29.4 - - + +
91A PHE 2.9 7.0 + - - +
93A LYS* 1.3 97.2 - - + +
95A GLY* 1.3 56.4 - - - +
124A ASP* 4.1 3.4 - - - +
127A ASP* 3.8 26.0 - - + +
128A ALA* 3.8 23.1 - - + +
131A ALA* 3.4 33.9 - - + +
132A MET* 3.5 32.1 - - + +
135A ALA* 5.2 4.9 - - - +
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Residues in contact with GLY 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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91A PHE 3.1 6.5 + - - +
92A GLU* 3.2 24.9 - - - +
93A LYS 3.4 1.2 - - - -
94A TYR* 1.3 78.5 - - - +
96A ARG* 1.3 61.3 + - - -
97A VAL 3.0 8.4 + - - -
119A PHE* 3.6 14.2 - - - -
124A ASP* 3.5 14.1 - - - -
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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