Contacts of the strand formed by residues 14 - 19 (chain D) in PDB entry 2P80
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 14 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200C GLY* 2.6 20.9 - - - -
10D LYS* 2.3 55.2 + - - +
11D GLY 2.8 9.7 + - - -
13D GLU* 1.3 75.4 - - - +
15D ALA* 1.3 60.6 + - - -
17D VAL* 3.8 4.6 - - - +
114D ARG* 4.5 1.1 - - - -
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Residues in contact with ALA 15 (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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93C LEU* 5.5 5.5 - - + +
141C MET* 2.7 32.0 - - + +
144C TRP* 3.5 13.7 - - + -
200C GLY* 3.8 4.4 + - - -
203C TYR* 3.3 24.5 - - + +
9D ASN 3.2 6.1 - - - -
10D LYS* 3.3 1.2 - - - +
14D GLY* 1.3 73.5 - - - -
16D MET* 1.3 56.9 + - - +
84D MET 4.3 1.2 - - - +
114D ARG* 2.9 32.1 + - - +
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Residues in contact with MET 16 (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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140C GLY* 3.1 16.2 - - - +
141C MET* 3.1 48.0 - - + -
203C TYR* 4.3 1.8 - - - +
8D LEU 3.4 0.7 - - - -
9D ASN* 2.7 41.8 + - + +
14D GLY 3.9 0.2 + - - -
15D ALA* 1.3 75.9 - - - +
17D VAL* 1.3 59.3 + - - +
40D HIS* 3.2 22.7 - - + -
81D HIS* 3.6 31.6 - - + +
84D MET* 4.5 6.3 - - + -
86D MET* 3.4 24.8 - - + +
114D ARG* 3.1 13.3 + - - +
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Residues in contact with VAL 17 (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 HIS 3.7 0.3 - - - +
7D MET* 3.6 0.2 - - - -
8D LEU* 2.9 39.8 + - + +
10D LYS 4.2 0.9 - - - -
11D GLY* 3.8 31.4 - - - +
13D GLU* 4.4 12.6 - - + +
14D GLY 3.8 9.0 - - - +
15D ALA 3.6 3.8 - - - +
16D MET* 1.3 76.5 - - - +
18D PHE* 1.3 64.6 + - - +
19D GLU* 4.2 13.9 + - + +
86D MET* 3.3 14.1 - - - +
87D ILE 5.7 0.2 - - - +
114D ARG* 3.1 35.0 - - - +
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Residues in contact with PHE 18 (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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5D VAL* 4.1 13.9 - - + -
6D HIS 3.4 1.3 - - - -
7D MET* 2.8 43.7 - - + -
17D VAL* 1.3 76.1 - - - +
19D GLU* 1.3 64.9 + - - +
20D PRO 3.5 19.4 - - - +
21D ALA* 3.6 10.7 + - - +
33D PHE* 4.3 6.1 - + - -
41D ASN 3.5 19.7 - - - -
42D VAL* 3.8 12.8 - - + -
76D VAL* 5.0 2.7 - - + -
77D LYS 4.1 4.7 - - - -
78D CYS* 3.7 14.4 - - + -
86D MET* 3.2 35.4 - - + -
87D ILE* 3.6 24.6 + - - +
88D ALA* 4.0 15.3 - - + -
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Residues in contact with GLU 19 (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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4D GLU 4.3 0.5 - - - +
5D VAL* 3.4 1.2 - - - +
6D HIS* 2.8 40.6 + - + +
8D LEU* 3.3 31.0 - - + +
11D GLY* 3.4 6.4 - - - -
12D ALA* 3.0 35.8 + - + +
13D GLU 4.9 0.3 + - - -
17D VAL* 4.3 7.2 - - + +
18D PHE* 1.3 78.4 - - - +
20D PRO* 1.3 64.7 - - + +
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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