Contacts of the strand formed by residues 125 - 133 (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 TRP 125 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49B LEU* 3.8 6.8 - - + +
52B GLU* 3.2 6.5 - - - -
53B GLU 2.9 33.5 + - - +
55B ILE* 4.5 13.5 - - + -
72B VAL* 3.3 37.3 - - + +
73B GLY* 3.2 46.9 - - - +
74B SER* 4.1 10.3 - - - -
83B ASP 5.4 4.7 - - - -
85B GLU* 4.0 29.6 - - + -
87B LEU* 5.2 1.5 - - + +
120B ALA* 3.0 26.7 + - + -
121B ALA* 5.8 0.2 - - - -
123B LYS* 3.8 38.0 + - + -
124B ARG* 1.3 83.5 - - - +
126B ASP* 1.3 63.0 + - - +
127B ARG 4.2 3.4 - - - +
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Residues in contact with ASP 126 (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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48B GLN* 3.5 2.2 - - - +
49B LEU* 2.7 45.9 + - + +
51B LYS* 4.2 3.1 - - - -
52B GLU* 3.9 26.0 - - + +
73B GLY 3.1 4.0 + - - -
74B SER* 3.1 10.9 + - - -
75B SER* 2.7 48.4 + - - -
125B TRP* 1.3 75.0 - - - +
127B ARG* 1.3 65.8 + - - +
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Residues in contact with ARG 127 (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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10B VAL* 3.3 47.1 - - - +
46B VAL* 3.9 4.7 - - + -
47B LEU 3.3 9.2 - - - -
48B GLN* 4.0 7.3 - - - +
49B LEU* 4.3 1.0 - - - +
72B VAL* 3.4 4.0 - - - +
73B GLY 2.8 31.9 + - - +
74B SER 3.7 10.1 + - - +
75B SER* 4.0 26.7 + - - +
79B ALA* 3.3 31.7 - - - +
84B TYR* 3.6 16.5 + - + +
125B TRP* 4.2 1.7 - - - +
126B ASP* 1.3 94.5 - - - +
128B VAL* 1.3 71.7 + - - +
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Residues in contact with VAL 128 (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* 5.0 4.0 - - + -
45B VAL 3.6 2.8 - - - +
46B VAL* 4.4 2.2 - - - +
47B LEU* 2.9 51.9 + - + +
49B LEU* 5.1 13.5 - - + -
55B ILE* 4.2 8.3 - - + -
70B VAL* 4.8 1.1 - - + -
71B LEU 3.4 7.4 - - - +
72B VAL* 3.8 18.2 - - + -
125B TRP* 5.9 0.2 - - + -
127B ARG* 1.3 80.8 - - - +
129B LYS* 1.3 62.3 + - - +
130B ILE* 3.7 4.5 + - + +
149B PHE* 3.7 44.0 - - + -
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Residues in contact with LYS 129 (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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44B SER* 3.6 22.2 - - - +
45B VAL 3.3 12.1 - - - +
46B VAL* 4.4 13.0 - - + +
69B GLU 3.9 0.2 - - - +
70B VAL* 3.4 3.3 - - - +
71B LEU* 2.7 58.1 + - + +
80B GLY 5.2 1.1 + - - -
81B GLU* 3.8 32.7 + - - +
84B TYR* 4.1 34.3 - - + -
128B VAL* 1.3 71.3 - - - +
130B ILE* 1.3 62.2 + - - +
131B VAL* 4.2 7.6 - - + -
303D VAL* 4.2 22.6 - - + +
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Residues in contact with ILE 130 (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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24B LEU* 5.0 1.8 - - + -
33B TRP* 3.9 4.3 - - + -
43B ILE 3.9 0.5 - - - +
44B SER* 3.4 4.7 - - - -
45B VAL* 3.0 48.4 + - + +
47B LEU* 4.6 9.0 - - + -
60B ILE* 5.6 0.9 - - + -
68B VAL* 4.2 11.9 - - + -
69B GLU 3.4 9.0 - - - +
70B VAL* 4.4 9.2 - - + -
128B VAL* 4.2 5.8 - - + +
129B LYS* 1.3 79.2 - - - +
131B VAL* 1.3 63.7 + - - +
132B CYS* 4.5 3.8 - - - -
144B LEU* 3.8 26.5 - - + -
147B VAL* 4.1 22.9 - - + -
149B PHE* 3.8 30.7 - - + -
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Residues in contact with VAL 131 (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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42B THR* 4.5 19.5 - - + +
43B ILE 3.5 10.3 - - - +
44B SER* 4.6 7.6 - - - +
67B PHE 3.9 0.7 - - - +
68B VAL* 3.4 4.5 - - - +
69B GLU* 2.9 49.0 + - + +
71B LEU* 3.9 25.4 - - + -
129B LYS* 4.5 10.8 - - + -
130B ILE* 1.3 73.9 - - - +
132B CYS* 1.3 63.0 + - - +
133B SER* 4.1 7.6 + - - +
303D VAL* 4.1 22.2 - - + -
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Residues in contact with CYS 132 (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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33B TRP* 3.9 12.1 - - - -
42B THR* 3.1 5.1 - - - -
43B ILE* 2.8 53.6 + - + -
65B SER* 3.4 21.3 - - - +
67B PHE 3.6 3.4 - - - -
68B VAL* 4.4 7.4 - - - -
130B ILE* 4.0 1.3 + - - -
131B VAL* 1.3 75.5 - - - +
133B SER* 1.3 60.8 + - - +
142B PHE* 3.7 4.0 - - + -
143B GLY 4.3 2.0 - - - -
144B LEU* 3.3 43.3 - - - -
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Residues in contact with SER 133 (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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41B LYS 3.4 9.2 - - - -
42B THR* 4.0 13.5 - - - +
65B SER* 3.6 2.4 - - - -
66B ALA 2.7 30.8 + - - -
67B PHE* 3.0 37.6 + - - +
90B THR* 5.5 2.4 - - - +
131B VAL* 4.6 8.5 + - - +
132B CYS* 1.3 75.3 + - - +
134B GLN* 1.3 56.4 + - - +
135B PRO* 4.1 4.0 - - - -
142B PHE* 4.3 1.8 - - - -
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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