Contacts of the strand formed by residues 27 - 32 (chain D) in PDB entry 3MPZ
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 GLY 27 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10D ALA* 3.4 23.9 - - - +
13D VAL* 3.6 5.4 - - - -
14D SER* 3.4 7.6 - - - -
26D VAL* 1.3 75.1 - - - +
28D ALA* 1.3 60.3 + - - +
40D GLY 3.5 7.0 - - - -
54D ALA* 4.0 2.9 - - - -
75D CYS* 3.3 4.9 - - - -
76D VAL 2.9 35.0 + - - -
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Residues in contact with ALA 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ALA* 4.0 3.4 - - - -
13D VAL* 3.6 4.6 - - - +
27D GLY* 1.3 75.4 - - - +
29D ALA* 1.3 61.0 + - - +
39D THR* 3.3 3.5 - - - -
40D GLY 2.8 31.2 + - - +
54D ALA* 3.8 20.4 - - + -
55D GLU* 4.1 13.9 - - + +
58D VAL* 3.7 18.8 - - + -
73D LEU* 4.6 4.3 - - + -
74D SER 3.1 11.4 - - - +
75D CYS* 4.4 4.3 - - + -
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Residues in contact with ALA 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D LEU* 3.5 35.4 - - + +
9D LYS* 3.7 15.0 - - + -
10D ALA* 3.6 10.9 - - - +
28D ALA* 1.3 76.6 - - - +
30D ALA* 1.3 62.0 + - - +
37D THR* 4.0 2.0 - - + -
38D VAL 3.2 9.9 - - - +
39D THR* 4.1 2.2 - - + -
58D VAL* 4.4 0.9 - - - -
73D LEU* 3.3 3.7 - - - +
74D SER 2.9 31.8 + - - +
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Residues in contact with ALA 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D LEU* 3.8 5.6 - - - +
29D ALA* 1.3 75.6 - - - +
31D LEU* 1.3 59.1 + - - +
32D VAL 3.7 0.5 + - - -
36D ARG 3.7 0.3 - - - +
37D THR* 3.2 3.7 - - - +
38D VAL* 2.8 36.7 + - + +
58D VAL* 3.7 26.0 - - + -
70D LEU* 3.9 18.6 - - + -
72D ALA 3.1 14.4 - - - +
73D LEU* 4.1 11.2 - - + -
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Residues in contact with LEU 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0D MET 5.5 1.6 - - - +
1D VAL* 4.0 33.4 - - + -
2D ASN 5.6 0.7 - - - +
6D LEU* 3.8 11.7 - - + +
30D ALA* 1.3 71.3 - - - +
32D VAL* 1.3 66.1 + - - +
35D GLY* 3.9 18.4 - - - +
36D ARG 3.6 14.4 - - - +
37D THR* 4.3 9.6 - - - +
70D LEU* 3.7 2.8 - - - -
71D VAL* 2.8 42.4 + - + +
72D ALA* 2.9 18.1 + - + +
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Residues in contact with VAL 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D ALA 4.0 0.4 - - - +
31D LEU* 1.3 82.5 - - - +
33D ASP* 1.3 71.5 + - - +
34D ASP* 3.0 28.3 - - - +
35D GLY* 2.9 21.1 + - - -
36D ARG* 2.9 19.2 + - + +
38D VAL* 4.0 30.3 - - + -
62D LEU* 3.5 32.8 - - + -
68D GLY* 4.1 2.5 - - - -
69D ARG 3.4 13.5 - - - +
70D LEU* 4.1 4.3 - - + -
71D VAL* 4.2 3.0 - - - +
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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