Contacts of the strand formed by residues 34 - 43 (chain B) in PDB entry 3KDH
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 34 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29B GLU 4.5 1.0 + - - -
31B ASP* 3.1 36.2 + - + +
32B PRO 3.3 0.4 - - - +
33B THR* 1.3 93.8 - - - +
35B CYS* 1.3 65.1 + - - +
36B THR* 4.2 14.4 - - - +
150B THR* 5.3 4.0 - - - -
151B VAL 3.2 13.2 - - - +
152B ASP* 3.6 22.2 - - - +
153B ILE* 3.6 9.4 - - - +
159B GLU* 3.6 14.0 - - - +
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Residues in contact with CYS 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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34B THR* 1.3 75.1 - - - +
36B THR* 1.3 65.1 + - - +
149B TYR* 3.7 15.0 - - - +
150B THR* 3.3 4.9 - - - -
151B VAL* 2.8 46.0 + - + +
153B ILE* 3.9 13.0 - - + +
159B GLU* 4.3 11.9 - - + +
162B THR* 4.5 5.4 - - + -
163B LYS* 3.2 51.1 - - - -
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Residues in contact with THR 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B PHE* 3.4 41.4 - - + -
29B GLU 4.2 14.8 + - - +
34B THR* 4.2 9.8 + - - +
35B CYS* 1.3 81.4 - - - +
37B SER* 1.3 62.4 + - - +
149B TYR* 3.2 7.0 - - - -
150B THR* 3.5 26.2 - - + -
159B GLU* 5.4 1.0 + - - -
163B LYS* 2.7 21.2 + - - -
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Residues in contact with SER 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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36B THR* 1.3 75.9 - - - +
38B LEU* 1.3 63.3 + - - +
39B ILE* 4.0 4.3 - - - +
147B GLU 4.0 0.5 - - - +
148B SER* 3.1 7.4 - - - -
149B TYR* 3.0 47.7 + - - -
163B LYS* 3.3 16.7 + - - +
167B ASP* 2.8 35.0 + - - -
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Residues in contact with LEU 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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7B VAL* 4.5 20.9 - - + -
8B LYS 5.9 0.5 + - - -
22B ILE* 4.1 36.8 - - + -
26B HIS* 4.1 11.4 - - + +
37B SER* 1.3 76.3 + - - +
39B ILE* 1.3 71.8 + - - +
40B THR* 4.4 9.0 + - + +
146B LEU* 4.0 22.2 - - + -
147B GLU 3.7 12.8 - - - +
148B SER* 3.9 15.5 - - - -
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Residues in contact with ILE 39 (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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37B SER* 4.0 2.9 - - - +
38B LEU* 1.3 82.1 - - - +
40B THR* 1.3 70.5 + - - +
145B VAL 3.9 0.3 - - - +
146B LEU* 3.5 2.9 - - - -
147B GLU 2.8 39.1 + - - +
149B TYR* 4.6 7.4 - - + -
167B ASP* 3.5 41.7 - - + +
170B VAL* 3.7 25.1 - - + -
171B LYS* 3.9 34.8 - - + +
174B LEU* 4.0 11.9 - - + +
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Residues in contact with THR 40 (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 VAL* 3.9 10.3 - - + -
8B LYS 2.9 27.9 + - - +
9B GLY* 3.8 10.0 - - - -
10B LEU* 3.9 22.3 - - + +
38B LEU* 4.5 8.3 - - + +
39B ILE* 1.3 80.2 - - - +
41B GLN* 1.3 63.1 + - - +
144B VAL* 4.7 0.4 - - - -
145B VAL 3.4 6.7 - - - -
146B LEU* 3.4 25.6 - - + -
171B LYS* 2.8 26.9 + - - +
174B LEU* 4.3 2.2 - - - -
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Residues in contact with GLN 41 (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 LEU* 5.7 0.2 - - - -
40B THR* 1.3 76.5 - - - +
42B ARG* 1.3 83.5 + - - +
43B ILE* 3.8 13.5 + - + +
143B THR 3.7 0.5 - - - +
144B VAL* 3.4 5.4 - - - -
145B VAL* 2.9 40.9 + - + +
171B LYS* 2.9 28.9 + - - +
174B LEU* 3.6 39.3 - - + +
175B GLN* 3.3 29.2 + - - +
178B GLY* 5.5 2.4 - - - -
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Residues in contact with ARG 42 (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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9B GLY 3.1 24.3 + - - +
10B LEU* 4.0 7.2 - - + +
11B THR* 4.2 10.4 - - - +
14B GLU* 2.8 39.6 + - - -
41B GLN* 1.3 92.9 + - - +
43B ILE* 1.3 60.4 + - - +
44B HIS* 3.9 28.9 + - - +
142B TYR* 3.5 34.3 - - + -
143B THR 3.4 3.4 - - - +
144B VAL* 4.4 5.7 - - + +
171B LYS* 5.2 0.6 - - - +
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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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41B GLN* 3.8 15.7 - - + +
42B ARG* 1.3 79.2 - - - +
44B HIS* 1.3 63.5 + - - +
45B ALA* 2.9 10.3 + - + +
50B VAL* 4.0 21.8 - - + -
142B TYR* 3.4 1.9 - - - +
143B THR* 2.8 46.5 + - - +
145B VAL* 3.8 25.6 - - + -
177B LEU* 3.9 14.8 - - + -
178B GLY* 3.6 35.7 - - - +
181B ALA* 4.1 1.6 - - + -
182B THR* 3.8 20.0 - - + -
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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