Contacts of the helix formed by residues 30 - 39 (chain B) in PDB entry 1A7A
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 PRO 30 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B GLU 4.4 0.6 - - - +
27B ASN 4.7 3.6 - - - +
28B GLU* 3.1 15.3 - - - +
29B MSE 1.3 84.3 - - - +
31B GLY* 1.3 58.3 + - - +
33B MSE 3.8 7.2 - - + +
34B ARG* 2.8 35.0 + - + +
356B PHE* 4.2 3.8 - - + -
397B ALA 3.9 13.7 - - - +
398B HIS* 3.5 23.8 - - + -
401B LYS* 4.0 29.4 - - + +
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Residues in contact with GLY 31 (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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29B MSE 2.9 1.6 + - - -
30B PRO* 1.3 78.5 - - - +
32B LEU* 1.3 57.3 + - - -
34B ARG* 2.7 26.9 + - - +
35B MSE 3.0 11.6 + - - +
359B SER* 2.9 13.6 + - - -
363B THR* 3.3 19.5 - - - +
397B ALA* 4.5 5.8 - - - -
398B HIS* 3.4 12.9 + - - -
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Residues in contact with LEU 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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29B MSE 3.3 16.2 + - + +
31B GLY* 1.3 72.7 - - - +
33B MSE 1.3 57.6 + - - +
35B MSE 3.0 9.9 + - - +
36B ARG* 2.9 31.4 + - - +
62B VAL* 3.7 30.3 - - + -
63B LEU* 3.8 22.0 - - + +
66B THR* 3.8 12.1 - - + +
359B SER* 3.5 8.9 + - - +
362B PHE* 3.4 49.6 - - + +
363B THR* 3.4 9.5 + - - +
366B VAL* 3.9 14.6 - - + -
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Residues in contact with MSE 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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26B GLU* 3.2 59.7 - - + +
29B MSE 3.1 12.9 + - - +
30B PRO* 4.0 8.1 - - + +
31B GLY 3.1 0.6 - - - -
32B LEU* 1.3 80.5 - - - +
34B ARG* 1.3 61.0 + - - +
36B ARG* 3.2 38.8 + - + +
37B GLU* 3.2 29.4 + - - +
62B VAL* 4.4 9.0 - - - -
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Residues in contact with ARG 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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30B PRO* 2.8 21.9 + - + +
31B GLY* 2.7 12.1 + - - +
33B MSE 1.3 70.5 - - - +
35B MSE 1.3 67.2 + - - +
37B GLU* 3.4 38.7 + - - +
38B ARG* 3.3 54.6 + - - +
397B ALA* 4.8 19.0 - - + +
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Residues in contact with MSE 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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31B GLY 3.0 8.4 + - - +
32B LEU* 3.3 13.7 - - - +
34B ARG* 1.3 79.1 - - - +
36B ARG* 1.3 62.2 + - - +
38B ARG* 3.2 11.5 + - - +
39B TYR* 3.0 61.3 + - + +
66B THR* 4.5 6.7 - - + -
70B LEU* 4.7 3.6 - - + -
363B THR* 4.4 10.1 - - + +
366B VAL* 3.7 23.1 - - + -
367B MSE 3.2 49.1 - - + +
370B ILE* 4.0 14.6 - - + -
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Residues in contact with ARG 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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26B GLU* 3.4 11.9 + - - -
32B LEU 2.9 16.9 + - - +
33B MSE 3.2 45.4 - - + +
34B ARG 3.2 0.2 - - - -
35B MSE 1.3 77.3 - - - +
37B GLU* 1.3 56.5 + - - +
40B SER* 2.8 36.9 + - - -
62B VAL* 2.8 37.6 + - - +
65B GLU* 3.4 25.6 + - - +
66B THR* 2.8 30.6 + - + +
69B THR* 4.3 19.9 + - + -
70B LEU* 4.2 7.9 - - - -
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Residues in contact with GLU 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 MSE 3.2 20.4 - - - +
34B ARG* 3.4 40.3 + - - +
36B ARG* 1.3 77.7 - - - +
38B ARG* 1.3 56.7 + - - +
40B SER* 4.7 4.0 - - - -
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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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34B ARG* 3.3 41.8 + - - +
35B MSE 3.2 15.5 + - - +
36B ARG 3.1 1.0 - - - -
37B GLU* 1.3 80.2 - - - +
39B TYR* 1.3 99.5 + - + +
40B SER 3.8 0.4 - - - -
41B ALA* 5.3 2.7 + - - +
42B SER* 4.3 4.2 + - - -
367B MSE 5.7 4.0 - - - +
390B LEU* 5.9 5.9 - - - +
393B ALA* 6.2 2.0 - - - +
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Residues in contact with TYR 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 MSE 3.0 52.8 + - + +
38B ARG* 1.3 131.2 + - + +
40B SER* 1.3 64.6 + - - +
41B ALA 3.1 3.4 - - - -
42B SER* 3.6 12.3 - - - -
43B LYS* 2.9 22.5 + - - -
44B PRO* 3.3 33.7 - - + +
70B LEU* 3.6 16.1 - - + -
370B ILE* 4.1 20.4 - - + +
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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