Contacts of the strand formed by residues 18 - 27 (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 GLY 18 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14B ASP* 3.7 3.6 - - - +
15B THR* 2.3 38.2 + - - +
16B PRO 3.3 1.8 + - - -
17B GLN* 1.3 81.5 - - - +
19B THR* 1.3 63.6 + - - -
38B PRO* 4.5 7.2 - - - -
39B GLN 4.8 1.8 - - - -
84B ARG* 3.9 22.0 - - - -
85B ALA* 5.3 2.5 - - - +
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Residues in contact with THR 19 (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* 4.5 3.2 - - - -
13B ARG 3.1 9.4 + - - -
14B ASP* 3.6 17.5 - - - +
15B THR* 4.5 0.4 - - - -
18B GLY* 1.3 73.4 - - - -
20B GLU* 1.3 66.0 + - - +
21B VAL* 3.8 3.1 + - - +
38B PRO* 3.9 4.4 - - - +
39B GLN* 3.0 49.5 + - + +
40B GLU* 4.9 0.2 - - - -
41B SER* 4.5 8.3 - - - +
84B ARG 3.4 15.9 - - - +
86B HIS* 4.4 10.1 - - - +
110B PRO* 4.2 20.0 - - + +
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Residues in contact with GLU 20 (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* 3.1 24.3 - - - -
13B ARG* 2.7 50.8 + - + +
15B THR* 4.1 15.8 + - - +
19B THR* 1.3 72.5 - - - +
21B VAL* 1.3 62.4 + - - +
22B SER* 3.7 8.2 + - - -
35B THR* 3.7 27.1 - - + +
36B LEU 4.8 4.9 - - - +
38B PRO* 5.5 2.7 - - + -
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Residues in contact with VAL 21 (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 3.6 4.7 - - - +
19B THR* 3.8 4.2 + - - +
20B GLU* 1.3 77.5 - - - +
22B SER* 1.3 59.4 + - - +
23B PHE* 3.1 39.2 - - + -
34B VAL 4.1 0.2 - - - +
35B THR* 3.5 3.1 - - - +
36B LEU* 2.8 52.3 + - + +
37B ALA 5.1 0.4 + - - -
39B GLN* 4.2 17.5 - - + -
110B PRO* 3.8 37.2 - - + +
111B PRO* 3.9 11.9 - - + -
114B TYR* 5.3 0.9 - - + -
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Residues in contact with SER 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ARG* 3.4 0.2 - - - -
11B HIS* 2.7 56.9 + - - +
20B GLU* 4.7 11.5 + - - -
21B VAL* 1.3 74.6 - - - +
23B PHE* 1.3 71.2 + - - +
24B TRP* 5.0 0.7 + - - -
33B GLN* 3.4 25.6 + - - +
34B VAL 3.4 7.8 + - - -
35B THR* 4.5 4.5 + - - +
270B LYS* 5.6 1.4 + - - -
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Residues in contact with PHE 23 (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* 4.2 10.1 - - + -
9B THR 3.2 10.3 - - - +
10B ARG* 3.3 37.5 - - + +
11B HIS* 4.5 1.1 - - - -
21B VAL* 3.1 31.0 - - + -
22B SER* 1.3 74.6 - - - +
24B TRP* 1.3 66.8 + - - +
25B LEU* 4.1 15.9 - - + -
33B GLN* 3.7 2.8 - - - +
34B VAL* 2.9 39.4 + - + +
36B LEU* 3.4 21.1 - - + -
111B PRO* 4.1 8.3 - - + -
114B TYR* 4.7 0.2 - + - -
115B LEU* 3.5 39.5 - - + -
140B LEU* 4.2 20.0 - - + -
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Residues in contact with TRP 24 (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* 3.6 3.1 - - - -
8B LEU* 2.9 25.8 + - + +
9B THR* 3.0 11.9 + - + +
11B HIS* 3.1 29.8 - + - -
22B SER* 5.0 0.4 - - - -
23B PHE* 1.3 77.2 - - - +
25B LEU* 1.3 61.8 + - - +
31B PRO* 4.2 15.9 - - + -
32B LEU 3.3 17.5 - - - -
33B GLN* 3.7 41.5 - - + +
248B ARG* 3.6 53.4 - - + -
249B ASP* 4.4 10.5 - - + -
270B LYS* 3.2 26.9 - - + +
271B GLY* 3.8 20.4 - - - +
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Residues in contact with LEU 25 (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 GLY* 4.4 5.2 - - - -
6B PHE 3.3 14.4 - - - +
7B ILE* 4.1 26.2 - - + -
8B LEU* 4.4 7.1 - - - +
23B PHE* 4.4 9.4 - - + -
24B TRP* 1.3 78.5 - - - +
26B ALA* 1.3 60.2 + - - +
27B THR* 4.1 9.0 - - + -
31B PRO* 3.2 8.7 - - - +
32B LEU* 2.8 43.7 + - + +
34B VAL* 3.6 27.1 - - + -
124B VAL* 4.2 12.6 - - + -
126B VAL* 3.5 30.3 - - + -
140B LEU* 4.9 5.8 - - + -
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Residues in contact with ALA 26 (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 GLY* 3.0 5.0 - - - -
6B PHE 2.8 33.0 + - - +
8B LEU* 4.1 10.8 - - + -
25B LEU* 1.3 72.4 - - - +
27B THR* 1.3 61.9 + - - +
30B GLY 4.1 3.4 - - - -
31B PRO* 4.7 1.8 - - - -
146B TYR* 3.7 5.0 - - - -
148B PRO* 3.4 27.6 - - + -
149B PRO 4.7 3.4 - - - +
150B LEU* 4.1 17.7 - - + -
218B ASP* 5.0 4.5 - - - +
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Residues in contact with THR 27 (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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3B GLN* 4.2 11.2 + - - +
4B ALA 3.8 16.8 - - - +
5B GLY* 4.0 5.6 - - - -
25B LEU* 4.1 4.5 - - + -
26B ALA* 1.3 85.7 - - - +
28B ASP* 1.3 63.2 + - - +
29B ASN* 2.9 16.4 + - - +
30B GLY* 2.6 34.8 + - - +
31B PRO 4.9 0.7 - - - -
32B LEU* 4.0 30.0 - - + +
146B TYR* 3.4 11.2 - - - -
149B PRO* 3.9 13.2 - - - +
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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