Contacts of the strand formed by residues 65 - 69 (chain A) in PDB entry 2KAI
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 VAL 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A VAL* 3.6 11.0 - - + -
32A ALA 3.8 3.4 - - - -
33A ILE* 4.0 21.1 - - + -
52A VAL* 4.0 4.7 - - + -
63A TYR* 4.0 3.1 - - + -
64A GLU* 1.3 74.6 - - - +
66A TRP* 1.3 59.2 + - - +
67A LEU* 3.2 27.6 - - + -
81A GLN 4.0 0.5 - - - +
82A PHE* 3.7 1.7 - - - -
83A PHE* 2.8 38.7 + - + +
85A VAL* 4.1 20.6 - - + -
106B LEU* 4.2 11.7 - - + -
108B LEU* 3.6 25.6 - - + -
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Residues in contact with TRP 66 (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 GLN 4.9 0.2 - - - +
31A VAL* 3.7 1.4 - - - -
32A ALA* 2.9 46.8 + - + +
34A TYR* 3.5 30.6 - + - +
38A SER* 4.8 11.0 + - - -
64A GLU* 3.8 15.6 - - + +
65A VAL* 1.3 73.9 - - - +
67A LEU* 1.3 63.7 + - - +
69A GLY 4.5 0.2 + - - -
70A ARG* 3.6 42.3 + - - +
80A ALA* 4.5 13.7 - - + -
81A GLN 3.3 16.8 - - - -
82A PHE* 3.7 52.2 - + + -
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Residues in contact with LEU 67 (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 GLN 5.1 2.5 - - - -
31A VAL* 3.5 22.4 - - + -
46A LEU* 4.1 13.0 - - + -
52A VAL* 4.9 0.2 - - + -
65A VAL* 3.2 32.8 - - + -
66A TRP* 1.3 73.1 - - - +
69A GLY* 1.3 67.1 + - - +
70A ARG* 3.3 3.2 + - - +
80A ALA* 3.1 4.2 - - - +
81A GLN* 2.6 49.8 + - + +
83A PHE* 3.4 26.0 - - + -
108B LEU* 4.2 2.9 - - + -
112B ALA* 3.4 23.1 - - + -
118B VAL* 3.8 19.3 - - + -
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Residues in contact with GLY 69 (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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28A PRO 5.3 2.5 + - - -
30A GLN 4.5 10.1 + - - -
67A LEU* 1.3 75.8 - - - +
70A ARG* 1.3 59.0 + - - +
79A THR* 2.6 32.1 + - - -
80A ALA* 3.5 4.2 + - - +
117B ALA* 3.7 26.3 + - - +
118B VAL* 3.9 10.5 - - - +
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Residues in contact with ARG 70 (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 HIS* 3.6 13.9 + - - -
30A GLN 5.1 2.7 + - - +
32A ALA* 5.7 2.0 - - + -
34A TYR* 5.2 6.0 + - - -
66A TRP* 3.6 52.4 + - + -
67A LEU 3.3 5.3 - - - +
69A GLY* 1.3 78.0 - - - +
71A HIS* 1.3 62.0 + - - +
72A ASN 3.7 10.9 + - - +
73A LEU* 2.8 36.2 + - + +
74A PHE 4.4 1.4 - - - -
75A GLU 2.6 28.2 + - - +
76A ASN* 4.7 2.8 - - - +
77A GLU* 3.5 11.3 - - + +
80A ALA* 3.5 24.2 - - + +
141B TRP* 3.2 28.2 - - + -
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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