Contacts of the strand formed by residues 30 - 35 (chain E) in PDB entry 2Z7F
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 MET 30 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E TRP* 2.9 28.3 + - + +
28E PRO 4.6 2.4 - - - +
29E PHE* 1.3 82.3 - - - +
31E VAL* 1.3 79.6 + - - +
43E GLY* 4.1 4.7 - - - -
44E ALA 4.0 1.1 - - - +
67E VAL 4.5 0.7 - - - +
68E LEU* 4.8 0.2 - - - -
69E GLY* 4.5 14.9 + - - -
70E ALA 5.0 3.8 + - - +
139E MET* 3.9 14.6 - - - -
140E GLY* 4.1 9.9 - - - -
141E TRP* 3.6 37.5 - - + +
155E LEU* 3.9 17.3 - - + -
197E SER* 3.7 25.4 - - - +
198E PRO* 3.5 25.4 - - + -
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Residues in contact with VAL 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E PHE 3.4 16.2 - - - +
30E MET* 1.3 82.1 - - - +
32E SER* 1.3 69.8 + - - +
33E LEU* 4.2 1.1 - - + -
43E GLY* 3.3 6.9 - - - -
44E ALA* 3.0 48.5 + - + +
45E THR 4.0 0.2 - - - -
46E LEU* 3.6 16.8 - - + +
52E VAL* 4.0 6.7 - - + -
66E VAL* 3.6 26.9 - - + -
67E VAL 3.6 11.4 - - - +
68E LEU* 3.4 22.2 - - + -
141E TRP* 3.8 3.8 - - - -
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Residues in contact with SER 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E VAL* 1.3 74.4 - - - +
33E LEU* 1.3 58.7 + - - +
34E GLN* 3.0 27.3 + - - +
40E HIS* 2.8 25.2 + - - +
42E CYS 3.8 3.1 - - - -
65E ARG 3.6 0.9 - - - +
67E VAL* 2.8 46.3 + - - +
70E ALA* 5.2 0.2 - - - -
73E LEU* 4.0 6.6 - - - +
141E TRP* 3.7 19.2 - - - -
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Residues in contact with LEU 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E VAL* 4.2 7.9 - - + -
32E SER* 1.3 71.3 - - - +
34E GLN* 1.3 58.7 + - - +
40E HIS* 3.5 3.5 - - - -
41E PHE* 2.9 50.8 + - + -
42E CYS* 2.8 26.0 + - + +
43E GLY 4.0 2.0 - - - +
44E ALA* 4.0 20.2 - - + -
52E VAL* 4.7 1.1 - - + -
54E SER* 3.7 29.6 - - - +
58E CYS* 4.8 0.9 - - + -
59E VAL* 4.5 7.6 - - + -
65E ARG* 3.5 9.0 - - + -
66E VAL* 3.9 29.4 - - + -
106E LEU* 4.4 17.5 - - + -
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Residues in contact with GLN 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E SER* 3.0 25.2 + - - +
33E LEU* 1.3 80.0 - - - +
35E LEU* 1.3 60.9 + - - +
38E GLY* 3.6 25.8 + - - -
39E GLY 3.2 10.8 - - - +
40E HIS* 3.9 14.4 + - - +
41E PHE* 3.6 5.3 - - - -
64E ALA 3.9 0.7 - - - +
65E ARG* 2.8 53.8 + - - +
67E VAL* 3.6 27.0 - - + +
73E LEU* 4.1 14.9 - - - +
80E ARG* 4.9 9.1 + - - +
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Residues in contact with LEU 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E GLN* 1.3 71.8 - - - +
36E ARG* 1.3 77.7 + - + +
38E GLY 3.1 1.1 - - - -
39E GLY* 2.9 19.4 + - - +
41E PHE* 3.6 32.4 - - + -
62E VAL* 3.7 35.0 - - + +
64E ALA* 3.6 41.3 - - + +
65E VAL* 4.0 9.2 - - + +
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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