Contacts of the strand formed by residues 62 - 68 (chain A) in PDB entry 5KQF
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 TYR 62 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A LEU* 4.4 15.7 - - + -
55A ARG 3.4 6.5 - - - +
61A GLY* 1.3 80.8 - - - -
63A TYR* 1.3 60.9 + - - +
78A LEU* 3.4 5.5 - - - +
79A VAL* 2.8 34.3 + - + +
202A LEU* 3.7 45.1 - - + -
203A CYS 2.7 22.3 + - - -
204A GLY* 4.2 0.5 - - - -
218A VAL* 3.7 24.1 - - + +
219A GLY 3.2 31.0 - - - -
277A SER* 5.0 10.2 + - - +
383A ALA* 4.7 7.6 - - + -
387A GLU* 2.6 32.1 + - - +
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Residues in contact with TYR 63 (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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53A ASN 3.8 0.5 - - - +
54A LEU* 3.3 9.2 - - - -
55A ARG* 2.7 64.4 + - + +
56A GLY* 3.7 21.5 + - - -
57A LYS* 5.1 0.9 - - + -
61A GLY 4.7 0.9 - - - -
62A TYR* 1.3 75.2 - - - +
64A VAL* 1.3 61.2 + - - +
76A ASN* 3.5 32.3 - - + -
77A ILE 3.1 23.3 - - - +
78A LEU* 3.9 2.5 - - - +
79A VAL* 4.3 0.4 - - - +
162A ASN* 2.8 42.9 + - + +
163A TRP* 3.9 27.8 - + + -
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Residues in contact with VAL 64 (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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53A ASN* 3.7 29.2 - - + +
54A LEU* 3.7 15.3 - - + -
63A TYR* 1.3 75.4 - - - +
65A GLU* 1.3 71.5 + - - +
66A MET* 3.6 24.4 + - + -
76A ASN* 3.7 3.3 - - - -
77A ILE* 2.8 38.0 + - - +
79A VAL* 3.8 12.5 - - + +
135A ILE* 4.1 17.5 - - + -
137A HIS* 5.9 1.1 - - + -
167A LEU* 4.8 7.6 - - + -
222A MET* 5.2 7.9 - - + -
224A ILE* 5.7 0.2 - - + -
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Residues in contact with GLU 65 (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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53A ASN 4.4 3.4 + - - -
63A TYR* 5.2 0.4 - - - -
64A VAL* 1.3 76.6 - - - +
66A MET* 1.3 67.5 + - - +
67A THR* 5.4 0.2 - - - +
74A THR* 3.5 33.4 + - + +
75A LEU 3.7 5.2 - - - +
76A ASN* 3.9 13.5 + - - +
98A ARG* 5.3 1.2 + - - -
135A ILE* 3.6 11.8 - - - +
136A PRO* 3.2 39.1 - - + +
137A HIS* 4.6 19.8 + - + -
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Residues in contact with MET 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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64A VAL* 3.9 13.0 - - + -
65A GLU* 1.3 80.2 - - - +
67A THR* 1.3 68.0 + - - +
68A VAL* 5.4 2.0 - - + -
74A THR* 3.4 6.6 - - - +
75A LEU* 2.9 32.3 + - + +
77A ILE* 3.6 41.7 - - + -
86A PHE* 3.9 15.0 - - + -
133A VAL* 3.6 27.4 - - + -
134A SER 3.4 6.1 - - - +
135A ILE* 4.0 20.0 - - + -
136A PRO* 3.8 1.8 - - - -
167A LEU* 4.0 28.3 - - + -
184A PHE* 4.1 7.6 - - + -
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Residues in contact with THR 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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66A MET* 1.3 78.0 - - - +
68A VAL* 1.3 67.9 + - - +
69A GLY 5.5 0.2 + - - -
72A PRO* 3.7 29.5 - - + +
73A GLN 3.2 5.2 - - - +
74A THR* 4.1 17.7 - - - +
132A LEU 4.5 0.2 - - - -
133A VAL* 3.2 6.9 - - - +
134A SER* 2.8 53.0 + - - +
136A PRO* 3.9 20.0 - - + -
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Residues in contact with VAL 68 (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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66A MET* 5.4 2.7 - - + -
67A THR* 1.3 79.9 - - - +
69A GLY* 1.3 62.9 + - - +
73A GLN* 2.8 45.8 + - + +
75A LEU* 3.7 22.2 - - + -
86A PHE* 3.8 35.0 - - + -
88A VAL* 5.2 2.0 - - + -
100A TYR* 3.5 32.5 - - + -
132A LEU 3.4 4.7 - - - -
133A VAL* 4.1 6.3 - - + -
147A ILE* 4.1 10.1 - - + -
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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