Contacts of the strand formed by residues 141 - 152 (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 VAL 141 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44B HIS* 4.6 5.4 + - - +
45B ALA* 4.4 6.9 + - - -
46B PRO* 3.8 40.6 - - + -
132B GLU* 4.1 20.0 - - - +
133B PHE 3.2 10.5 - - - +
134B LEU* 4.0 20.0 - - + -
139B GLY 4.3 3.8 - - - +
140B LYS* 1.3 83.9 - - - +
142B TYR* 1.3 65.8 + - - +
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Residues in contact with TYR 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLU* 2.6 38.6 + - - +
42B ARG* 3.5 28.3 - - + -
43B ILE 3.4 12.6 - - - +
44B HIS* 3.6 24.2 - + + +
45B ALA 3.7 6.5 - - - +
132B GLU* 3.5 6.4 - - - +
133B PHE* 2.8 67.8 + + + +
134B LEU 5.5 0.2 - - - -
135B ASN* 4.9 20.6 - - + -
140B LYS 5.6 0.2 - - - -
141B VAL* 1.3 78.4 - - - +
143B THR* 1.3 65.6 + - - +
144B VAL* 3.9 5.8 - - + -
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Residues in contact with THR 143 (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 3.7 0.3 - - - +
42B ARG* 3.4 5.2 - - - +
43B ILE* 2.8 40.4 + - + -
45B ALA 2.8 21.3 + - - -
46B PRO 3.4 0.7 + - - -
47B ALA* 3.1 22.9 + - - +
50B VAL* 4.1 11.2 - - + -
130B VAL* 3.6 28.9 - - + -
131B ASN 3.3 7.6 + - - +
142B TYR* 1.3 74.9 + - - +
144B VAL* 1.3 73.8 + - - +
145B VAL* 3.9 11.4 - - + -
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Residues in contact with VAL 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 3.9 26.7 - - + -
14B GLU* 4.4 4.7 - - - +
18B LEU* 3.8 20.9 - - + -
40B THR* 4.7 0.7 - - - -
41B GLN 3.4 7.4 - - - +
42B ARG* 4.4 5.8 - - + -
131B ASN* 2.8 41.1 + - + -
133B PHE* 3.5 30.7 - - + -
142B TYR* 3.9 13.0 - - + -
143B THR* 1.3 78.8 - - - +
145B VAL* 1.3 65.1 + - - +
146B LEU* 3.9 15.3 - - + -
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Residues in contact with VAL 145 (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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39B ILE 3.9 0.5 - - - +
40B THR* 3.4 5.0 - - - -
41B GLN* 2.9 40.5 + - + +
43B ILE* 3.8 17.7 - - + -
50B VAL* 3.8 28.9 - - + -
54B ILE* 4.4 1.1 - - + -
128B THR* 3.6 23.1 - - + -
129B SER 3.3 10.1 - - - +
130B VAL* 4.4 5.2 - - + -
143B THR* 3.9 8.7 - - + -
144B VAL* 1.3 72.8 - - - +
146B LEU* 1.3 67.0 + - - +
174B LEU* 4.0 21.1 - - + +
177B LEU* 4.0 7.4 - - + -
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Residues in contact with LEU 146 (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* 4.2 1.8 - - + -
18B LEU* 4.2 15.7 - - + -
21B VAL* 4.1 11.0 - - + -
22B ILE* 3.7 28.7 - - + -
26B HIS* 3.4 12.7 - - + +
38B LEU* 4.0 11.4 - - + -
39B ILE 3.5 2.2 - - - -
40B THR* 3.4 30.1 - - + -
128B THR* 3.2 4.5 - - - +
129B SER* 2.8 49.4 + - - +
131B ASN* 3.8 15.5 - - - +
144B VAL* 3.9 14.6 - - + -
145B VAL* 1.3 76.7 - - - +
147B GLU* 1.3 60.5 + - - +
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Residues in contact with GLU 147 (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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38B LEU* 3.7 2.4 - - - +
39B ILE* 2.8 42.1 + - - +
63B TYR* 4.8 10.2 + - - -
64B LYS* 5.6 3.8 + - - -
112B PHE* 5.1 4.2 - - - -
124B TYR* 4.0 11.9 + - - +
126B SER* 3.3 19.2 + - - +
127B VAL 3.3 2.2 - - - +
128B THR* 3.5 23.1 + - + +
145B VAL 4.2 0.4 + - - -
146B LEU* 1.3 75.2 - - - +
148B SER* 1.3 65.4 + - - +
149B TYR* 5.1 1.1 - - + -
170B VAL* 3.7 28.5 - - + +
173B ASN* 6.0 1.0 - - - +
174B LEU* 3.4 30.7 - - + +
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Residues in contact with SER 148 (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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26B HIS* 2.8 43.6 + - - +
27B GLN 5.5 1.1 + - - -
37B SER 3.1 12.6 - - - -
38B LEU* 3.9 10.5 - - - -
126B SER* 3.3 4.9 + - - -
127B VAL* 2.9 44.2 + - - +
147B GLU* 1.3 76.4 - - - +
149B TYR* 1.3 63.7 + - - +
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Residues in contact with TYR 149 (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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35B CYS* 3.7 18.1 - - - -
36B THR* 3.2 6.6 - - - -
37B SER* 3.0 47.2 + - - +
39B ILE* 4.6 8.1 - - + -
124B TYR* 3.6 24.5 - + + +
125B LYS 3.1 12.8 - - - +
126B SER* 4.7 0.7 - - - -
147B GLU* 5.1 1.8 - - + -
148B SER* 1.3 76.7 - - - +
150B THR* 1.3 78.2 + - - +
151B VAL* 4.0 9.4 - - + -
163B LYS* 3.3 21.8 + - - -
166B VAL* 3.5 34.9 - - + +
167B ASP* 2.7 33.3 + - - -
170B VAL* 4.3 10.1 - - + -
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Residues in contact with THR 150 (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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27B GLN 5.7 2.5 - - - +
28B PHE* 5.6 6.3 - - + -
29B GLU 5.8 1.6 - - - +
34B THR* 5.3 6.1 - - - -
35B CYS 3.3 6.3 - - - -
36B THR* 3.5 20.2 - - + -
123B ASN 4.1 2.5 + - - -
124B TYR* 3.3 3.5 - - - -
125B LYS* 2.9 54.1 + - + +
149B TYR* 1.3 81.9 - - - +
151B VAL* 1.3 64.5 + - - +
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Residues in contact with VAL 151 (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* 3.2 5.0 - - - +
35B CYS* 2.8 47.4 + - + -
121B LEU* 3.8 29.8 - - + -
122B LYS 3.5 13.0 - - - +
123B ASN 4.2 2.9 - - - -
124B TYR* 3.9 23.8 - - + -
149B TYR* 4.0 20.0 - - + -
150B THR* 1.3 76.7 - - - +
152B ASP* 1.3 71.7 + - - +
162B THR* 4.3 13.0 - - + -
166B VAL* 4.4 7.0 - - + -
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Residues in contact with ASP 152 (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 THR* 3.6 10.8 - - - +
34B THR* 3.6 17.4 - - - +
121B LEU* 4.3 2.4 - - - +
122B LYS* 2.9 36.6 + - + +
123B ASN* 2.8 33.8 + - - +
151B VAL* 1.3 84.7 - - - +
153B ILE* 1.3 65.5 + - - +
154B PRO* 3.4 10.2 - - - +
162B THR* 4.8 0.3 - - - +
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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