Contacts of the strand formed by residues 33 - 39 (chain B) in PDB entry 3KDM
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 ALA 33 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32B TYR* 1.3 76.4 - - - +
34B MET* 1.3 60.9 + - - +
51B ILE 3.0 17.7 - - - +
52B SER* 4.3 2.7 - - - -
53B GLY 4.1 3.2 - - - +
98B ARG* 3.6 4.3 - - - +
99B ASP* 3.0 30.4 + - + +
101B GLY 5.0 1.4 + - - -
105B TYR* 3.3 38.2 - - + +
226B TES 4.4 18.2 - - + -
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Residues in contact with MET 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 4.3 17.7 - - + -
22B CYS* 4.3 1.3 - - - -
29B PHE* 3.9 20.4 - - + -
32B TYR* 4.8 1.3 - - - +
33B ALA* 1.3 81.2 - - - +
35B SER* 1.3 53.7 + - - +
50B ALA* 2.7 17.2 - - - +
51B ILE* 2.6 52.4 + - + +
70B ILE* 3.9 1.5 - - - +
72B ARG* 2.9 31.6 - - - +
79B LEU* 3.2 36.6 - - + -
97B ALA 3.6 24.0 - - - +
98B ARG* 3.8 17.9 - - - -
99B ASP 5.5 0.2 - - - -
226B TES 5.1 1.3 - - - -
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Residues in contact with SER 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 MET* 1.3 76.3 - - - +
36B TRP* 1.3 71.9 + - - +
47B TRP* 3.1 31.2 + - - -
49B SER 3.1 5.4 - - - -
50B ALA* 4.5 3.4 - - - -
79B LEU* 4.1 1.2 - - - +
96B CYS* 3.3 6.2 - - - +
97B ALA* 2.6 36.1 + - - +
109B MET* 3.4 31.4 - - - -
226B TES 4.7 6.1 - - - -
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Residues in contact with TRP 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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6B GLU* 3.6 22.7 - - - -
20B LEU* 3.4 40.2 - - + -
21B SER 4.2 2.9 - - - -
22B CYS* 4.0 11.9 - - + -
35B SER* 1.3 80.9 + - - +
37B VAL* 1.3 63.0 + - - +
48B VAL* 2.9 33.4 + - + -
49B SER* 2.9 12.9 + - - +
70B ILE* 3.6 24.2 - - + -
79B LEU* 3.2 29.0 - - + +
80B TYR 3.3 22.4 + - - -
81B LEU* 3.6 41.5 - - + +
94B TYR* 4.3 6.5 - - + -
95B TYR 3.2 21.3 - - - -
96B CYS* 3.7 12.1 - - + -
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Residues in contact with VAL 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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102A PHE* 3.9 29.8 - - + -
35B SER* 3.8 12.3 - - - +
36B TRP* 1.3 78.9 - - - +
38B ARG* 1.3 70.3 + - - +
45B LEU* 4.1 12.8 - - + -
46B GLU 3.3 13.2 - - - +
47B TRP* 4.1 7.4 - - + -
48B VAL* 4.0 2.7 - - - -
93B VAL 4.0 0.2 - - - +
94B TYR* 3.7 1.8 - - - +
95B TYR* 2.9 32.7 + - + +
97B ALA* 5.8 0.9 - - + -
109B MET* 4.1 16.6 - - + -
112B TRP* 4.0 26.2 - - + -
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Residues in contact with ARG 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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37B VAL* 1.3 77.6 - - - +
39B GLN* 1.3 63.3 + - - +
40B ALA 4.2 0.9 - - - +
44B GLY 3.7 0.7 - - - +
45B LEU* 3.6 1.7 - - - -
46B GLU* 2.7 81.4 + - + +
48B VAL* 3.6 13.8 - - + +
63B SER* 3.9 16.2 + - - -
64B VAL* 4.5 14.1 - - - +
68B PHE* 4.6 0.6 - - - -
89B GLU* 4.6 9.6 + - - +
90B ASP* 2.8 37.5 + - - +
92B ALA* 4.0 10.8 - - + -
93B VAL 3.2 11.4 - - - +
94B TYR* 3.1 44.8 + - + -
95B TYR* 5.0 0.7 - - - -
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Residues in contact with GLN 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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40A GLN* 2.8 43.0 + - - -
89A TYR* 3.4 11.5 + - - -
38B ARG* 1.3 77.0 - - - +
40B ALA* 1.3 71.1 + - - +
41B PRO* 3.5 2.1 - - + +
42B GLY 5.5 1.1 - - - +
43B LYS 3.2 28.3 + - - +
44B GLY 3.6 6.6 - - - +
45B LEU* 3.6 15.3 - - + +
92B ALA* 3.5 3.3 - - - -
93B VAL* 2.9 37.8 + - + +
95B TYR* 3.6 14.1 + - + -
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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