Contacts of the strand formed by residues 2 - 15 (chain B) in PDB entry 3K5N
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 ALA 2 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0B HIS* 5.1 0.2 - - - -
1B MET* 1.3 81.0 - - + +
3B GLN* 1.3 63.1 + - - +
125B TRP* 3.8 24.6 - - + -
127B GLU* 3.7 34.3 - - + +
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Residues in contact with GLN 3 (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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1B MET* 4.0 2.3 + - + +
2B ALA* 1.3 75.5 - - - +
4B ALA* 1.3 63.8 + - - +
27B THR* 4.2 18.0 + - + -
28B ASP 5.7 0.2 - - - +
29B ASN* 5.2 11.1 - - - +
32B LEU* 3.4 29.9 - - + +
125B TRP* 3.7 5.8 - - - -
126B VAL* 2.5 54.4 + - + +
135B ILE* 4.3 10.7 - - - +
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Residues in contact with ALA 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B GLN* 1.3 82.5 + - - +
5B GLY* 1.3 59.1 + - - +
27B THR* 3.8 17.2 - - - -
28B ASP 4.9 0.9 + - - -
124B VAL 3.1 6.1 - - - -
125B TRP* 3.6 10.5 - - + +
126B VAL* 5.0 0.2 - - - -
143B HIS* 3.3 37.5 - - + +
146B TYR* 3.7 23.6 - - + -
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Residues in contact with GLY 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B GLN 4.0 0.6 + - - -
4B ALA* 1.3 74.6 - - - +
6B PHE* 1.3 61.0 + - - -
25B LEU* 4.3 10.0 - - - +
26B ALA 3.0 14.6 - - - -
27B THR* 4.0 8.1 - - - -
123B PRO* 3.8 0.5 - - - +
124B VAL* 2.8 31.9 + - - +
146B TYR* 3.1 16.4 - - - -
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Residues in contact with PHE 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B GLY* 1.3 75.0 - - - +
7B ILE* 1.3 74.6 + - - +
8B LEU* 3.3 7.1 + - + +
25B LEU* 4.0 2.2 - - - +
26B ALA* 2.8 29.0 + - - +
122B SER* 3.5 27.4 - - - -
123B PRO* 3.7 24.5 - - + -
146B TYR* 3.7 14.4 - - + -
147B ARG* 4.0 12.3 - - - -
148B PRO* 3.6 42.8 - - + -
353B LEU* 3.8 39.3 - - + -
356B ALA* 5.0 0.4 - - + -
357B THR* 3.7 8.3 - - - -
363B VAL* 4.2 10.8 - - + -
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Residues in contact with ILE 7 (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 PHE* 1.3 84.2 - - - +
8B LEU* 1.3 60.5 + - - +
9B THR 4.1 14.8 - - - +
10B ARG* 3.1 39.9 + - - +
23B PHE* 4.2 11.4 - - + -
24B TRP 3.6 8.7 - - - +
25B LEU* 4.1 18.8 - - + +
115B LEU* 4.3 8.5 - - + -
120B ILE* 5.6 0.7 - - + -
121B THR 4.0 13.5 - - - +
122B SER* 2.8 26.0 + - - +
124B VAL* 4.1 14.1 - - + -
140B LEU* 5.2 5.4 - - + -
363B VAL* 4.9 4.5 - - - +
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Residues in contact with LEU 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B PHE* 3.3 8.7 + - + +
7B ILE* 1.3 77.6 - - - +
9B THR* 1.3 63.0 + - - +
10B ARG* 5.8 1.1 - - - -
24B TRP* 2.9 12.9 + - + +
25B LEU 4.4 3.4 - - - +
26B ALA* 4.1 18.4 - - + +
150B LEU* 4.0 23.3 - - + -
218B ASP* 3.8 29.6 - - + +
248B ARG* 3.8 2.0 - - - +
271B GLY* 2.7 33.9 - - - +
272B ARG* 4.2 1.5 - - - +
273B LEU* 3.2 40.3 - - + +
353B LEU* 6.0 0.7 - - + -
362B PRO* 5.7 4.0 - - - +
363B VAL* 5.5 2.7 + - - +
364B ASP* 4.2 4.7 - - - +
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Residues in contact with THR 9 (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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7B ILE* 3.5 2.9 - - - +
8B LEU* 1.3 82.2 + - - +
10B ARG* 1.3 67.5 + - - +
11B HIS* 2.3 49.6 - - + +
23B PHE* 3.2 7.1 - - - +
24B TRP* 3.0 23.3 + - + +
269B ALA 4.2 2.9 + - - -
270B LYS* 3.9 0.5 - - - -
271B GLY* 2.8 30.7 + - - -
272B ARG 3.8 7.6 + - - -
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Residues in contact with ARG 10 (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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7B ILE* 3.1 35.6 + - - +
8B LEU 5.8 0.8 + - - -
9B THR* 1.3 77.8 - - - +
11B HIS* 1.3 77.7 + - - +
22B SER 3.4 5.2 - - - -
23B PHE* 3.3 23.1 - - + -
111B PRO* 3.9 15.3 - - + -
112B GLU* 4.2 23.9 + - - +
115B LEU* 3.8 19.3 - - - +
121B THR 4.3 5.5 + - - -
122B SER* 4.5 5.3 + - - -
360B GLY 3.0 27.5 + - - -
362B PRO* 4.1 34.4 - - + +
375B HIS* 5.1 1.4 - - - -
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Residues in contact with HIS 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B THR* 2.3 36.9 + - + +
10B ARG* 1.3 81.9 - - - +
12B TRP* 1.3 66.3 + - - +
13B ARG* 6.6 0.2 - - - -
21B VAL* 3.6 0.2 - - - -
22B SER* 2.7 48.5 + - - +
24B TRP* 3.1 27.5 - + - -
111B PRO* 3.5 10.5 - - - +
270B LYS* 3.2 35.3 - - + +
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Residues in contact with TRP 12 (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 HIS* 1.3 79.7 - - - +
13B ARG* 1.3 78.0 + - - +
14B ASP* 3.9 17.7 - - - -
19B THR* 4.5 3.6 - - - +
20B GLU 3.1 11.2 - - - +
21B VAL* 4.5 0.9 - - + -
22B SER* 5.5 0.2 - - - -
86B HIS* 3.7 35.4 - + + -
87B ARG* 3.9 37.5 - - + -
90B MET* 4.6 6.3 - - - -
109B ARG* 4.0 19.3 - - + +
110B PRO* 3.9 25.1 - - + +
111B PRO* 3.4 33.7 - - + -
112B GLU* 5.5 0.2 - - - -
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Residues in contact with ARG 13 (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 HIS* 6.6 0.4 - - - -
12B TRP* 1.3 93.4 - - - +
14B ASP* 1.3 63.2 + - - +
15B THR* 3.6 27.1 + - + +
19B THR* 3.1 2.3 - - - -
20B GLU* 2.7 61.8 + - + +
87B ARG* 5.9 1.6 - - - +
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Residues in contact with ASP 14 (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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12B TRP* 3.9 6.5 - - - -
13B ARG* 1.3 76.0 + - - +
15B THR* 1.3 66.4 + - - +
18B GLY 3.8 2.9 - - - +
19B THR* 3.6 13.3 - - - -
85B ALA* 3.6 13.8 - - + -
86B HIS 3.1 24.2 + - - -
87B ARG* 3.1 44.4 + - - +
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Residues in contact with THR 15 (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 ARG* 3.6 44.0 - - + +
14B ASP* 1.3 81.3 - - - +
16B PRO* 1.3 78.2 - - + +
17B GLN* 4.2 5.0 + - - +
18B GLY* 2.3 39.3 + - - +
19B THR 4.5 0.2 - - - -
20B GLU* 4.1 22.0 + - - +
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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