Contacts of the strand formed by residues 34 - 43 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A GLU 4.4 2.9 + - - -
31A ASP* 2.9 40.2 + - + +
32A PRO 4.5 0.2 - - - -
33A THR* 1.3 93.7 - - - +
35A CYS* 1.3 66.0 + - - +
36A THR* 4.2 13.3 - - - +
150A THR* 5.3 4.9 - - - -
151A VAL 3.2 13.0 - - - -
152A ASP* 3.5 20.6 - - - +
153A ILE* 3.4 14.2 - - - +
159A GLU* 3.8 8.7 - - - +
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Residues in contact with CYS 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A THR* 1.3 76.4 - - - +
36A THR* 1.3 66.7 + - - +
149A TYR* 4.0 8.0 - - - -
150A THR* 3.4 1.2 - - - -
151A VAL* 2.8 45.2 + - - -
153A ILE* 4.0 4.0 - - + +
159A GLU* 3.9 28.5 - - + +
162A THR* 3.5 32.5 - - - -
163A LYS* 3.9 21.8 - - + -
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Residues in contact with THR 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A PHE* 3.2 49.4 - - + -
29A GLU 5.0 4.9 - - - +
34A THR* 4.2 12.1 - - - +
35A CYS* 1.3 81.1 - - - +
37A SER* 1.3 63.6 + - - +
149A TYR* 3.2 12.6 - - - -
150A THR* 3.7 24.9 - - + -
159A GLU* 5.3 1.2 + - - -
163A LYS* 3.0 22.9 + - - +
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Residues in contact with SER 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PRO* 5.1 5.2 - - - -
36A THR* 1.3 79.5 + - - +
38A LEU* 1.3 63.5 + - - +
39A ILE* 3.7 5.9 - - - +
148A SER* 3.2 6.1 - - - -
149A TYR* 3.1 43.0 + - - +
163A LYS* 3.4 19.9 + - - +
167A ASP* 2.9 32.3 + - - -
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Residues in contact with LEU 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PRO* 3.7 29.5 - - + +
6A ALA 4.0 12.3 + - - +
7A VAL* 3.8 33.9 - - + -
8A LYS* 5.4 4.7 + - - +
22A ILE* 4.0 18.6 - - + -
26A HIS* 4.1 7.4 - - + +
37A SER* 1.3 78.2 + - - +
39A ILE* 1.3 73.5 + - - +
40A THR* 4.4 6.1 + - + +
146A LEU* 3.9 19.1 - - + -
147A GLU 3.6 25.1 - - - +
148A SER* 4.0 9.6 - - - -
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Residues in contact with ILE 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A SER* 3.7 3.1 - - - +
38A LEU* 1.3 82.3 - - - +
40A THR* 1.3 66.0 + - - +
145A VAL 3.8 0.7 - - - +
146A LEU* 3.6 3.5 - - - -
147A GLU 2.8 37.8 + - - +
149A TYR* 4.6 5.6 - - + -
167A ASP* 3.5 41.3 - - + +
170A VAL* 3.7 25.6 - - + -
171A LYS* 4.0 32.8 - - + +
174A LEU* 3.9 17.5 - - + +
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Residues in contact with THR 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A VAL* 4.3 9.0 - - + -
8A LYS 2.7 32.6 + - - +
9A GLY* 3.9 8.8 + - - -
10A LEU* 3.9 24.3 - - + +
38A LEU* 4.6 7.9 - - + +
39A ILE* 1.3 78.5 - - - +
41A GLN* 1.3 61.6 + - - +
145A VAL 3.4 4.7 - - - -
146A LEU* 3.5 26.5 - - + -
171A LYS* 2.9 26.0 + - - +
174A LEU* 4.3 2.0 - - - -
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Residues in contact with GLN 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LEU* 5.8 0.4 - - - -
40A THR* 1.3 75.9 - - - +
42A ARG* 1.3 79.0 + - - +
43A ILE* 3.8 15.0 + - + +
143A THR 3.8 0.7 - - - +
144A VAL* 3.5 4.9 - - - +
145A VAL* 2.9 38.6 + - + +
171A LYS* 2.7 37.5 + - - +
174A LEU* 3.6 38.8 - - + +
175A GLN* 3.3 26.1 + - - +
178A GLY* 5.6 1.8 - - - -
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Residues in contact with ARG 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A GLY 3.8 19.8 + - - -
10A LEU* 4.1 5.6 - - + +
11A THR* 5.1 6.6 - - - +
14A GLU* 3.2 30.4 + - - -
41A GLN* 1.3 92.4 + - - +
43A ILE* 1.3 61.7 + - - +
44A HIS* 3.9 32.9 + - + +
142A TYR* 3.8 32.7 - - + -
143A THR 3.4 4.0 - - - -
144A VAL* 4.6 4.2 - - + +
171A LYS* 5.2 0.4 - - - +
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Residues in contact with ILE 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A GLN* 3.8 15.3 - - + +
42A ARG* 1.3 79.9 - - - +
44A HIS* 1.3 65.1 + - - +
45A ALA* 2.9 17.9 + - + +
50A VAL* 4.0 17.5 - - + -
142A TYR* 3.5 1.9 - - - +
143A THR* 2.8 41.1 + - - +
145A VAL* 3.7 26.0 - - + -
177A LEU* 4.0 14.8 - - + -
178A GLY* 3.7 40.2 - - - +
181A ALA* 4.1 1.8 - - + -
182A THR* 3.9 14.8 - - + -
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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