Contacts of the strand formed by residues 71 - 77 (chain B) in PDB entry 1K7E
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 THR 71 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B THR* 3.4 30.8 + - + +
69B THR* 3.1 12.4 + - - +
70B ARG* 1.3 79.3 - - - +
72B THR* 1.3 74.6 + - - +
73B LEU* 4.4 4.3 - - + +
358B ALA 5.6 0.2 - - - +
362B MET* 3.3 28.3 + - + +
365B GLN 5.2 0.5 + - - -
366B PRO 5.6 0.3 + - - -
368B LYS 4.4 0.7 + - - -
370B GLN* 3.3 27.3 + - - -
372B LEU* 4.1 24.5 - - + -
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Residues in contact with THR 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LYS* 4.1 14.8 - - + -
66B THR* 4.5 3.1 - - - -
70B ARG 4.7 2.4 + - - -
71B THR* 1.3 79.8 + - - +
73B LEU* 1.3 61.6 + - - +
74B TYR* 3.9 24.5 - - + -
220B GLU* 4.0 12.9 + - - +
370B GLN 2.8 10.0 + - - +
371B LEU* 3.6 14.8 - - + +
372B LEU* 3.0 25.9 + - - +
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Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LYS* 3.6 7.7 - - - +
62B CYS* 3.2 32.5 + - + +
65B ILE* 4.0 31.0 - - + -
66B THR* 3.7 18.3 + - + +
71B THR* 4.6 3.8 - - + -
72B THR* 1.3 76.9 - - - +
74B TYR* 1.3 75.4 + - - +
75B LEU* 4.6 5.2 - - + -
339B LEU* 6.5 0.2 - - + -
355B LEU* 4.1 18.4 - - + -
358B ALA* 4.1 12.8 - - + -
359B LEU* 5.1 1.8 - - + -
362B MET* 6.0 0.7 - - - -
372B LEU* 3.3 14.4 - - + +
374B VAL* 3.7 29.8 - - + +
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Residues in contact with TYR 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU* 3.7 35.9 - - + -
60B THR 3.1 4.7 - - - -
61B LYS* 3.5 45.8 + - + +
72B THR* 3.9 13.5 - - + -
73B LEU* 1.3 81.7 - - - +
75B LEU* 1.3 63.8 + - - +
76B LYS 4.1 0.2 - - - -
216B ILE* 3.6 21.3 - - + -
219B LYS* 3.8 28.9 + - + +
220B GLU* 2.3 39.1 + - + +
371B LEU* 4.0 8.1 - - + -
372B LEU 2.9 8.4 + - - +
373B VAL* 3.3 7.3 - - + -
374B VAL 2.8 24.6 + - - -
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU* 3.5 4.0 - - - -
60B THR* 2.8 37.2 + - - +
62B CYS* 3.6 26.0 - - - -
73B LEU* 4.6 4.7 - - + -
74B TYR* 1.3 75.8 - - - +
76B LYS* 1.2 63.8 + - - +
77B ARG* 3.5 14.4 + - - +
339B LEU* 4.0 20.0 - - + -
345B ILE* 3.7 29.8 - - + -
355B LEU* 4.6 15.9 - - + -
374B VAL* 3.3 30.5 - - + +
376B LEU* 4.2 19.7 - - + -
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Residues in contact with LYS 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ARG* 3.7 2.5 - - - +
57B THR* 2.7 33.1 + - - +
58B ALA 3.6 6.7 - - - +
59B LEU* 3.8 9.8 - - + +
74B TYR 4.1 0.2 - - - -
75B LEU* 1.2 71.5 - - - +
77B ARG* 1.3 58.7 + - - +
78B GLU* 3.0 17.6 + - - +
208B ILE* 3.5 25.6 - - + +
211B GLU* 2.9 22.0 + - - +
212B THR* 3.7 17.0 - - - +
215B GLN* 2.8 25.5 + - - +
240B MET* 4.9 0.7 - - - -
373B VAL* 4.4 4.9 - - + +
374B VAL 3.0 9.9 + - - +
375B ASN* 3.5 24.8 + - - +
376B LEU* 2.8 29.3 + - - +
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Residues in contact with ARG 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B THR* 3.2 18.9 - - - +
58B ALA* 2.9 29.5 + - + +
60B THR* 2.9 41.1 + - - +
75B LEU* 3.6 26.5 - - - +
76B LYS* 1.3 71.3 - - - +
78B GLU* 1.4 58.9 + - - +
79B ASP* 2.6 46.7 + - - +
80B LEU* 3.0 49.1 + - + +
345B ILE* 3.6 28.2 - - - +
376B LEU* 4.1 5.1 - - - +
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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
------------------------------------------------------------
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