Contacts of the strand formed by residues 42 - 53 (chain B) in PDB entry 3K75
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 42 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13B SER* 4.9 0.5 + - - -
40B GLU* 3.9 7.6 - - - +
41B LYS* 1.3 93.2 + - + +
43B ILE* 1.3 72.6 + - - +
44B SER* 6.0 0.3 - - - -
131B VAL* 4.5 12.9 - - + +
132B CYS 3.1 12.1 - - - -
133B SER* 4.0 15.3 - - - +
142B PHE* 4.3 0.7 - - - -
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Residues in contact with ILE 43 (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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13B SER* 3.5 7.4 - - - +
14B SER* 3.7 12.8 - - - +
33B TRP* 3.5 35.2 - - + +
35B ALA* 3.7 23.8 - - + +
40B GLU* 3.5 19.1 - - - +
42B THR* 1.3 81.5 - - - +
44B SER* 1.3 62.5 + - - +
130B ILE 3.9 0.2 - - - +
131B VAL* 3.5 5.8 - - - +
132B CYS* 2.8 42.7 + - + +
142B PHE* 3.6 30.5 - - + +
143B GLY* 4.0 11.2 - - - -
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Residues in contact with SER 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B CYS* 3.3 0.2 - - - -
13B SER* 2.6 43.7 + - - -
33B TRP* 3.4 4.5 - - - -
42B THR* 6.0 0.4 - - - -
43B ILE* 1.3 77.8 - - - +
45B VAL* 1.3 74.5 + - - +
46B VAL* 5.3 0.9 - - - +
129B LYS* 3.6 32.1 - - - +
130B ILE 3.4 7.9 + - - -
131B VAL* 4.6 8.1 - - - +
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Residues in contact with VAL 45 (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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11B SER 3.5 5.6 - - - +
12B CYS* 3.5 16.8 - - + +
21B ALA* 3.8 11.9 - - + -
24B LEU* 3.9 16.4 - - + -
33B TRP* 3.2 35.9 - - + -
44B SER* 1.3 81.7 + - - +
46B VAL* 1.3 67.7 + - - +
47B LEU* 4.7 9.4 - - + -
128B VAL 3.6 0.3 - - - +
129B LYS* 3.3 9.0 - - - +
130B ILE* 3.0 51.8 + - + -
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Residues in contact with VAL 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL* 3.5 4.0 - - - +
10B VAL* 2.6 53.7 + - + -
11B SER* 3.0 30.1 + - - +
44B SER* 5.3 0.9 - - - +
45B VAL* 1.3 78.5 - - - +
47B LEU* 1.3 60.5 + - - +
84B TYR* 3.2 32.3 - - + +
127B ARG* 3.9 12.8 - - + -
128B VAL 3.7 6.1 - - - +
129B LYS* 4.4 16.4 - - + -
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Residues in contact with LEU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 3.9 36.3 - - + -
8B HIS 3.4 8.3 - - - +
9B VAL* 3.4 31.9 - - + -
10B VAL* 4.0 2.2 - - - -
24B LEU* 4.4 31.0 - - + -
25B LEU* 4.8 4.0 - - + -
45B VAL* 4.7 10.1 - - + -
46B VAL* 1.3 76.2 - - - +
48B GLN* 1.3 64.1 + - - +
49B LEU* 5.2 0.2 - - - +
127B ARG* 3.3 6.2 - - - +
128B VAL* 2.9 50.3 + - + +
130B ILE* 4.6 9.9 - - + -
147B VAL* 4.6 2.9 - - + -
149B PHE* 4.9 0.4 - - + -
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Residues in contact with GLN 48 (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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6B LEU* 4.1 3.3 - - - -
7B ARG* 3.1 20.7 + - - +
8B HIS* 3.0 44.0 + - + +
10B VAL* 3.5 19.5 - - + +
47B LEU* 1.3 75.1 - - - +
49B LEU* 1.3 66.4 + - - +
126B ASP* 3.5 6.3 - - - +
127B ARG* 4.0 8.3 - - - +
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Residues in contact with LEU 49 (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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4B ILE* 3.8 23.1 - - + -
5B ARG 4.0 2.5 - - - +
6B LEU* 3.8 28.9 - - + -
7B ARG* 3.6 12.7 - - - +
48B GLN* 1.3 80.4 - - - +
50B GLU* 1.3 64.1 + - - +
51B LYS* 3.2 17.3 + - - +
53B GLU* 4.1 16.8 - - + +
55B ILE* 5.7 4.5 - - + -
125B TRP* 3.8 11.2 - - + +
126B ASP* 2.7 40.2 + - - +
127B ARG* 4.3 3.1 - - - +
128B VAL* 5.1 16.8 - - + -
149B PHE* 5.7 2.7 - - + -
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Residues in contact with GLU 50 (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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5B ARG* 3.4 69.5 + - + +
6B LEU 4.5 4.5 - - - +
7B ARG* 3.7 32.2 - - + +
49B LEU* 1.3 74.0 - - - +
51B LYS* 1.3 65.6 + - + +
53B GLU* 5.5 2.5 - - - +
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Residues in contact with LYS 51 (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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49B LEU* 3.2 12.9 - - - +
50B GLU* 1.3 85.3 - - + +
52B GLU* 1.3 82.4 + - + +
53B GLU* 3.0 22.6 + - + +
126B ASP* 4.2 7.2 - - - -
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Residues in contact with GLU 52 (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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51B LYS* 1.3 87.3 - - + +
53B GLU* 1.3 59.0 + - - +
74B SER* 4.2 15.0 + - - +
76B ALA* 5.8 2.8 - - - +
124B ARG* 2.9 38.8 + - - +
125B TRP 3.2 13.7 - - - +
126B ASP* 3.9 20.8 - - + +
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Residues in contact with GLU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 3.0 55.1 - - + +
5B ARG* 4.3 4.3 + - - +
49B LEU* 4.1 5.2 - - + +
50B GLU* 5.5 1.6 - - - +
51B LYS* 3.5 20.9 + - + +
52B GLU* 1.3 74.6 - - - +
54B GLN* 1.3 63.1 + - - +
55B ILE* 3.9 6.4 + - - +
124B ARG* 3.5 18.6 - - - +
125B TRP 2.9 26.9 + - - +
151B SER* 3.8 14.3 + - - -
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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