Contacts of the strand formed by residues 86 - 94 (chain A) in PDB entry 2KKQ
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 GLY 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A ARG* 4.2 4.4 - - - +
52A ASN* 3.0 17.0 - - - -
84A ASP 3.8 1.8 + - - -
85A ALA* 1.3 76.4 - - - +
87A TRP* 1.3 67.9 + - - -
88A TYR* 3.7 10.4 - - - -
104A ARG* 4.3 0.6 - - - +
105A LEU* 3.2 30.9 + - - +
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Residues in contact with TRP 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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50A LYS 3.4 2.1 - - - +
51A ARG* 3.2 1.9 - - - -
52A ASN* 2.9 37.5 + - - +
86A GLY* 1.3 74.8 - - - -
88A TYR* 1.3 61.2 + - - +
89A THR* 4.6 4.1 + - - +
102A ASN* 4.3 21.3 - - + +
103A THR* 3.4 26.5 - - - -
104A ARG* 3.8 45.4 - - + +
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Residues in contact with TYR 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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35A LEU* 4.6 7.6 - - + -
49A TRP* 4.1 28.5 - + + -
50A LYS 3.0 6.7 - - - -
51A ARG* 3.4 41.8 + - + -
56A VAL* 4.3 16.4 - - + -
63A ILE* 4.9 5.6 - - + +
75A LEU* 4.3 7.9 - - + -
77A ILE* 3.4 30.0 - - + +
80A VAL* 5.1 0.2 - - - +
84A ASP* 3.5 10.1 + - - +
86A GLY 3.7 12.1 - - - -
87A TRP* 1.3 72.9 - - - +
89A THR* 1.3 64.2 + - - +
102A ASN* 3.4 3.5 + - - +
103A THR* 2.7 48.7 + - - +
105A LEU* 3.7 32.3 - - + +
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Residues in contact with THR 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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48A PHE 3.3 1.9 - - - +
49A TRP* 3.3 7.8 - - - -
50A LYS* 2.7 56.6 + - + +
87A TRP* 4.6 3.6 + - - +
88A TYR* 1.3 76.6 + - - +
90A VAL* 1.3 61.1 + - - +
91A SER* 4.7 3.4 + - - +
100A THR* 3.6 25.4 - - + -
101A CYS 3.6 4.5 - - - +
102A ASN* 2.8 29.7 + - - +
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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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18A PHE* 3.9 29.9 - - + -
22A PRO* 5.0 9.9 - - + -
37A CYS* 5.4 2.5 - - - -
39A ILE* 5.7 0.2 - - + -
47A LEU* 5.2 9.4 - - + -
48A PHE 3.1 7.9 - - - +
49A TRP* 3.7 45.9 - - + +
73A VAL* 5.2 4.3 - - + -
88A TYR 4.4 0.2 - - - -
89A THR* 1.3 72.3 - - - +
91A SER* 1.3 70.8 + - - +
100A THR* 3.3 3.7 - - - +
101A CYS* 2.9 52.0 + - + +
103A THR* 5.1 1.1 - - - +
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Residues in contact with SER 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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46A LYS 3.2 5.4 - - - +
47A LEU* 3.2 4.0 - - - +
48A PHE* 2.9 51.9 + - - +
89A THR* 4.7 3.8 + - - +
90A VAL* 1.3 74.5 - - - +
92A ALA* 1.3 60.7 + - - +
93A VAL* 6.2 0.9 - - - -
98A VAL* 5.5 3.8 - - - -
99A THR 3.6 4.0 - - - -
100A THR* 2.9 29.5 + - - +
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Residues in contact with ALA 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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16A PRO* 3.7 6.2 - - + +
18A PHE* 4.7 2.0 - - + -
39A ILE* 4.0 15.9 - - + -
45A PRO* 3.8 22.7 - - + -
46A LYS 3.3 4.5 - - - -
47A LEU* 3.8 13.0 - - + -
91A SER* 1.3 73.9 - - - +
93A VAL* 1.3 60.5 + - - +
98A VAL* 3.5 3.8 - - - -
99A THR* 2.9 45.3 + - + +
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Residues in contact with VAL 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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45A PRO* 3.5 4.3 - - - +
46A LYS* 3.1 45.5 + - + +
48A PHE* 3.7 17.5 - - + -
91A SER* 6.2 0.9 - - - -
92A ALA* 1.3 71.5 - - - +
94A ASN* 1.3 70.1 + - - +
98A VAL* 3.9 21.8 - - + -
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Residues in contact with ASN 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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14A ARG 3.3 21.1 + - - -
16A PRO* 3.7 13.7 - - + -
41A ALA* 4.2 1.4 - - - +
42A ILE 3.5 0.4 + - - +
43A PRO* 2.7 46.3 + - - +
44A PRO 5.6 0.2 - - - -
45A PRO* 3.8 11.1 - - + +
92A ALA 4.1 0.4 + - - -
93A VAL* 1.3 83.9 - - - +
95A GLU* 1.3 90.4 + - - +
96A ALA* 3.0 13.9 + - - +
97A GLY* 2.7 30.7 + - - +
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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
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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