Contacts of the helix formed by residues 30 - 39 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A GLU 4.4 1.1 - - - +
27A ASN 4.8 2.7 - - - +
28A GLU* 3.1 16.6 - - - +
29A MSE 1.3 84.0 - - - +
31A GLY* 1.3 57.9 + - - +
33A MSE 4.0 6.6 - - + +
34A ARG* 2.8 36.5 + - + +
356A PHE* 4.2 4.7 - - + -
397A ALA 3.8 13.9 - - - +
398A HIS* 3.4 23.8 - - + -
401A LYS* 4.0 27.6 - - + +
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Residues in contact with GLY 31 (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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29A MSE 2.9 2.0 + - - -
30A PRO* 1.3 77.4 - - - +
32A LEU* 1.3 56.4 + - - -
34A ARG* 2.7 27.5 + - - +
35A MSE 3.0 12.1 + - - +
359A SER* 2.9 13.7 + - - -
363A THR* 3.3 18.4 - - - +
397A ALA* 4.5 5.8 - - - -
398A HIS* 3.4 13.4 + - - -
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Residues in contact with LEU 32 (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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29A MSE 3.3 17.5 + - + +
31A GLY* 1.3 71.1 - - - +
33A MSE 1.3 58.8 + - - +
35A MSE 3.0 8.9 + - - +
36A ARG* 2.9 32.1 + - - +
62A VAL* 3.7 29.8 - - + -
63A LEU* 3.7 21.8 - - + +
66A THR* 3.8 11.0 - - - +
359A SER* 3.5 9.5 + - - +
362A PHE* 3.5 48.5 - - + +
363A THR* 3.4 7.1 + - - +
366A VAL* 3.9 17.0 - - + -
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Residues in contact with MSE 33 (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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26A GLU* 3.2 60.3 - - + +
29A MSE 3.1 14.0 + - - +
30A PRO* 4.0 7.4 - - + +
31A GLY 3.1 0.8 - - - -
32A LEU* 1.3 79.2 - - - +
34A ARG* 1.3 61.4 + - - +
36A ARG* 3.2 38.7 + - - +
37A GLU* 3.3 30.5 + - - +
62A VAL* 4.4 9.0 - - - -
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Residues in contact with ARG 34 (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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30A PRO* 2.8 23.1 + - + +
31A GLY* 2.7 14.4 + - - +
33A MSE 1.3 69.5 - - - +
35A MSE 1.3 64.8 + - - +
37A GLU* 3.4 38.8 + - - +
38A ARG* 3.3 55.2 + - - +
397A ALA* 4.8 19.0 - - + +
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Residues in contact with MSE 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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31A GLY 3.0 9.2 + - - +
32A LEU* 3.3 14.1 - - - +
34A ARG* 1.3 77.6 - - - +
36A ARG* 1.3 60.7 + - - +
38A ARG* 3.2 11.0 + - - +
39A TYR* 3.0 61.0 + - + +
66A THR* 4.5 6.5 - - + -
70A LEU* 4.7 3.4 - - + -
363A THR* 4.4 14.8 - - + -
366A VAL* 3.7 22.9 - - + -
367A MSE 3.2 45.5 - - + +
370A ILE* 4.0 15.0 - - + -
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Residues in contact with ARG 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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26A GLU* 3.5 11.5 + - - -
32A LEU 2.9 16.0 + - - +
33A MSE 3.2 45.9 - - + +
34A ARG 3.3 0.4 - - - -
35A MSE 1.3 76.0 - - - +
37A GLU* 1.3 58.5 + - - +
38A ARG 3.0 0.2 - - - -
40A SER* 2.8 36.8 + - - -
62A VAL* 2.8 36.0 + - - +
65A GLU* 3.3 27.6 + - - +
66A THR* 2.8 31.7 + - + +
69A THR* 4.4 19.7 + - + -
70A LEU* 4.3 8.5 - - - -
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Residues in contact with GLU 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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33A MSE 3.3 19.5 + - - +
34A ARG* 3.4 40.1 + - - +
36A ARG* 1.3 78.4 - - - +
38A ARG* 1.3 57.3 + - - +
39A TYR 3.7 0.2 - - - -
40A SER* 4.7 4.0 - - - -
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Residues in contact with ARG 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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34A ARG* 3.3 41.8 + - - +
35A MSE 3.2 15.3 + - - +
36A ARG 3.0 0.6 - - - -
37A GLU* 1.3 79.6 - - - +
39A TYR* 1.3 101.3 + - + +
40A SER 3.8 0.2 - - - -
41A ALA* 5.3 2.3 + - - +
42A SER* 4.3 4.2 + - - -
367A MSE 5.7 4.9 - - - +
390A LEU* 6.0 5.7 - - - +
393A ALA* 6.2 2.0 - - - +
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Residues in contact with TYR 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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35A MSE 3.0 53.2 + - + +
38A ARG* 1.3 132.7 + - + +
40A SER* 1.3 65.3 + - - +
41A ALA 3.1 3.1 - - - -
42A SER* 3.6 12.3 - - - -
43A LYS* 2.9 22.3 + - - -
44A PRO* 3.3 33.8 - - + +
70A LEU* 3.6 15.5 - - + +
370A ILE* 4.1 20.2 - - + +
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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