Contacts of the strand formed by residues 29 - 38 (chain B) in PDB entry 3K3K
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 SER 29 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B GLN 5.8 0.4 - - - -
26B ASP* 3.2 39.8 + - - +
27B PRO* 3.1 3.1 + - - +
28B GLY* 1.3 79.4 + - - +
30B CYS* 1.3 63.2 + - - +
144B VAL* 4.2 16.2 - - - +
145B VAL 3.3 9.0 - - - -
146B ASP* 3.1 18.3 + - - -
147B MET* 3.7 8.1 - - - +
153B GLU* 5.3 0.3 - - - +
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Residues in contact with CYS 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B SER* 1.3 75.6 - - - +
31B SER* 1.3 62.3 + - - +
143B TYR* 4.4 2.2 - - - -
144B VAL* 3.3 4.6 - - - +
145B VAL* 2.9 52.3 + - - +
147B MET* 3.8 23.6 - - - -
153B GLU* 4.0 13.2 - - - +
156B THR* 4.2 7.0 - - - -
157B ARG* 4.2 30.7 - - - +
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Residues in contact with SER 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TYR* 3.6 36.7 - - - +
30B CYS* 1.3 76.7 - - - +
32B SER* 1.3 56.2 + - - +
143B TYR* 3.1 19.7 - - - -
144B VAL* 4.1 5.6 - - - -
157B ARG* 2.7 31.6 + - - -
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Residues in contact with SER 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TYR* 5.6 1.1 - - - -
31B SER* 1.3 79.7 - - - +
33B LEU* 1.3 63.0 + - - +
34B HIS* 3.1 12.7 + - - -
141B GLU 4.0 0.3 - - - +
142B SER* 3.1 6.4 - - - -
143B TYR* 3.0 44.7 + - - -
157B ARG* 3.6 19.8 + - - +
161B ASP* 2.9 28.6 + - - -
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Residues in contact with LEU 33 (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 LEU* 6.2 1.1 - - + -
17B ILE* 3.8 33.4 - - + -
21B HIS* 3.8 43.3 - - + +
32B SER* 1.3 77.0 + - - +
34B HIS* 1.3 81.4 + - - +
35B ALA* 6.1 0.4 - - + -
140B LEU* 4.2 11.0 - - + -
141B GLU 3.6 13.5 - - - +
142B SER* 3.9 5.2 - - - -
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Residues in contact with HIS 34 (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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2B PRO* 6.3 2.7 - - + -
32B SER* 3.1 16.1 + - - -
33B LEU* 1.3 82.8 + - - +
35B ALA* 1.3 63.1 + - - +
140B LEU* 3.5 3.8 - - - -
141B GLU 2.8 35.2 + - - +
143B TYR* 4.5 4.3 - + - -
161B ASP* 3.1 35.3 + - - -
164B VAL* 3.8 17.4 - - + +
165B LYS* 2.8 54.9 + - + +
168B LEU* 3.7 21.3 - - + -
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Residues in contact with ALA 35 (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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2B PRO* 3.0 37.8 - - + +
5B LEU* 3.8 29.2 - - + +
33B LEU* 6.1 0.4 - - + -
34B HIS* 1.3 76.0 - - - +
36B GLN* 1.3 63.4 + - - +
138B VAL* 4.8 0.4 - - + -
139B VAL 3.3 6.3 - - - -
140B LEU* 3.7 19.7 - - + -
168B LEU* 4.4 4.9 - - - +
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Residues in contact with GLN 36 (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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2B PRO 3.5 26.7 + - - -
5B LEU* 6.3 0.2 - - - -
35B ALA* 1.3 76.6 - - - +
37B ARG* 1.3 83.5 + - - +
38B ILE* 3.8 12.9 + - + +
138B VAL* 3.5 5.2 - - - +
139B VAL* 2.8 41.9 + - + +
165B LYS 4.8 0.3 - - - +
168B LEU* 3.4 42.5 - - + +
169B GLN* 3.7 24.5 + - - +
172B ALA* 3.5 12.2 - - - +
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Residues in contact with ARG 37 (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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2B PRO 2.7 16.3 + - - +
3B SER* 3.9 21.7 + - - +
4B GLU 2.6 31.3 + - - +
5B LEU* 4.2 1.4 - - - +
6B THR* 4.0 9.9 - - - +
9B GLU* 2.9 33.2 + - - +
36B GLN* 1.3 92.9 + - - +
38B ILE* 1.3 63.4 + - - +
39B HIS* 3.8 30.3 + - + +
136B TRP* 3.5 29.4 - - + +
137B THR 3.5 3.4 - - - -
138B VAL* 4.5 5.1 - - + +
172B ALA* 4.1 2.1 - - - +
176B GLU* 4.4 2.3 - - - +
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Residues in contact with ILE 38 (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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36B GLN* 4.0 11.9 - - + +
37B ARG* 1.3 80.7 - - - +
39B HIS* 1.3 65.3 + - - +
40B ALA* 3.0 25.7 + - + +
45B VAL* 3.9 12.8 - - + -
136B TRP* 3.6 2.0 - - - +
137B THR* 2.8 41.7 + - - +
139B VAL* 3.7 26.0 - - + -
171B LEU* 3.8 24.9 - - + +
172B ALA* 3.8 20.4 - - + +
175B ALA* 3.9 12.8 - - + -
176B GLU* 3.6 9.6 - - + +
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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