Contacts of the helix formed by residues 31 - 41 (chain B) in PDB entry 3KQM
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 GLU 31 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29B ARG 3.2 9.4 + - - +
30B PHE* 1.3 73.8 - - - +
32B PRO* 1.3 72.0 - - + +
33B ARG* 3.2 2.5 - - + +
34B ALA* 2.9 21.7 + - + +
35B TYR* 3.0 11.8 + - - +
224B ALA 2.9 15.7 + - - +
225B GLY* 3.5 17.8 - - - -
226B GLU* 3.3 31.7 + - - +
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Residues in contact with PRO 32 (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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30B PHE* 3.4 22.9 - - + +
31B GLU* 1.3 82.4 - - + +
33B ARG* 1.3 58.4 + - + +
35B TYR* 3.2 3.2 + - + +
36B LEU* 2.9 34.5 + - - +
82B PRO* 4.3 4.1 - - + +
105B VAL* 3.9 29.4 - - + +
106B ASN* 3.2 26.7 - - - +
109B GLU* 4.1 20.9 - - + -
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Residues in contact with ARG 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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31B GLU* 3.1 2.3 + - + +
32B PRO* 1.3 79.4 - - + +
34B ALA* 1.3 62.7 + - - +
36B LEU* 3.4 14.8 + - - +
37B ARG* 3.0 32.1 + - - +
109B GLU* 2.8 33.7 + - + +
112B ARG* 4.4 7.0 - - - +
119B GLY 2.5 31.7 + - - -
120B ALA 3.5 1.4 + - - -
121B PHE* 3.4 29.2 - - - +
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Residues in contact with ALA 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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31B GLU* 2.9 16.7 + - - +
33B ARG* 1.3 78.2 - - - +
35B TYR* 1.3 58.1 + - - +
37B ARG* 3.3 23.6 + - - +
38B ASN* 2.8 39.8 + - - +
225B GLY* 3.4 35.7 - - - +
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Residues in contact with TYR 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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30B PHE* 3.4 36.8 - + + -
31B GLU 3.0 7.9 + - - +
32B PRO 3.6 5.2 - - - +
34B ALA* 1.3 74.5 - - - +
36B LEU* 1.3 68.7 + - - +
38B ASN* 3.2 3.2 + - - +
39B ASN* 3.0 56.3 + - - +
40B TYR* 3.8 11.7 - + - -
82B PRO* 3.9 13.5 - - + -
83B THR* 4.2 4.5 - - + -
222B TYR* 3.7 25.4 - + - -
223B LEU 4.9 0.2 - - - -
224B ALA* 4.2 7.7 - - + +
290B ES3 3.2 20.0 + + - -
2002B SAH 2.6 61.8 + - + +
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Residues in contact with LEU 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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32B PRO 2.9 21.0 + - - +
33B ARG* 3.7 23.1 - - - +
35B TYR* 1.3 78.1 - - + +
37B ARG* 1.3 58.3 + - - +
40B TYR* 2.8 33.3 + - + +
41B ALA 3.2 5.9 + - - -
82B PRO* 3.6 42.0 - - + +
83B THR* 4.2 4.3 - - + -
109B GLU* 4.5 6.7 - - - -
121B PHE* 3.7 41.2 - - + -
123B TRP* 3.6 25.4 - - + -
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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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33B ARG* 3.0 20.2 + - - +
34B ALA* 3.6 29.0 - - - +
36B LEU* 1.3 79.0 - - - +
38B ASN* 1.3 74.8 + - - +
39B ASN 3.3 0.7 + - - -
41B ALA* 3.3 34.3 + - + +
42B PRO 4.8 2.1 - - - +
121B PHE* 5.4 1.6 - - - -
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Residues in contact with ASN 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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34B ALA* 2.8 30.4 + - - +
35B TYR 3.2 4.0 + - - +
37B ARG* 1.3 88.1 + - - +
39B ASN* 1.3 70.3 + - - +
41B ALA 4.9 1.1 - - - +
43B PRO* 6.2 0.3 - - - +
44B ARG* 4.0 15.9 - - - +
223B LEU* 3.1 35.7 + - - +
224B ALA* 4.3 1.2 - - - +
225B GLY 4.6 3.4 - - - +
264B THR* 5.0 1.4 + - - -
266B VAL* 3.9 37.1 - - + +
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Residues in contact with ASN 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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35B TYR* 3.0 51.4 + - - +
38B ASN* 1.3 87.4 - - - +
40B TYR* 1.3 90.5 + - + +
41B ALA 3.9 0.7 - - - -
44B ARG* 3.4 48.7 + - - +
53B VAL* 5.7 0.7 - - - +
57B LYS* 4.9 2.9 + - - -
222B TYR* 5.0 4.2 - - - +
223B LEU 5.0 2.8 + - - -
266B VAL* 4.9 1.6 - - - +
267B ASP* 4.0 4.2 - - - +
290B ES3 3.7 19.9 - - + +
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Residues in contact with TYR 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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35B TYR* 3.8 8.5 - + - -
36B LEU* 2.8 21.2 + - - +
39B ASN* 1.3 92.3 - - + +
41B ALA* 1.3 62.1 + - - +
42B PRO* 4.7 0.2 - - - +
45B GLY* 3.0 7.1 - - - -
57B LYS* 3.0 36.2 + - + -
83B THR* 3.5 16.2 - - + -
85B TYR* 3.1 30.1 + + - -
121B PHE* 4.2 10.8 - - + -
123B TRP* 3.9 20.6 - + + -
126B TYR* 2.5 49.0 + + + +
290B ES3 3.4 6.1 - + - -
2002B SAH 2.6 30.6 + - - -
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Residues in contact with ALA 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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36B LEU 3.2 4.6 + - - +
37B ARG* 3.3 34.6 + - + +
38B ASN 4.9 1.0 - - - +
39B ASN 4.4 0.3 - - - -
40B TYR* 1.3 78.9 + - - +
42B PRO* 1.3 80.5 - - + +
43B PRO* 4.5 0.2 - - - +
44B ARG* 3.4 4.9 + - - +
45B GLY 2.8 13.5 + - - -
121B PHE* 4.6 8.7 - - + -
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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