Contacts of the strand formed by residues 21 - 28 (chain D) in PDB entry 2FRV
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 LEU 21 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12D ASP* 4.4 2.2 - - - -
13D PRO* 4.0 7.4 - - - +
14D ILE* 3.3 29.2 + - + +
17D ILE* 3.5 22.6 - - + +
19D GLY 3.6 3.8 + - - -
20D HIS* 1.3 73.7 - - - +
22D ARG* 1.3 68.2 + - - +
23D ILE* 4.1 17.5 - - + -
37D SER* 3.7 20.0 - - - +
38D MET 3.4 25.4 - - - +
39D SER* 4.1 9.0 - - - +
40D THR* 5.0 1.3 - - - -
490D LEU* 3.8 24.2 - - + -
524D VAL* 4.1 15.5 - - + -
529D PRO* 4.6 0.2 - - + -
531D ILE* 3.7 13.2 - - + -
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Residues in contact with ARG 22 (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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88C GLY 4.1 12.9 + - - -
10D VAL* 3.8 13.6 - - + +
11D VAL 3.5 5.4 - - - +
12D ASP* 3.1 41.4 + - + +
21D LEU* 1.3 76.2 - - - +
23D ILE* 1.3 63.0 + - - +
24D GLU* 2.7 35.3 + - + -
37D SER 4.0 0.2 - - - -
38D MET* 2.7 58.6 + - + +
40D THR* 4.1 3.8 - - + -
348D PHE* 3.5 33.5 - - - -
195I GLU 3.5 12.3 + - - -
196I ALA* 3.3 27.9 + - - +
197I GLY* 4.4 0.2 - - - -
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Residues in contact with ILE 23 (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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9D ILE 3.8 0.9 - - - +
10D VAL* 3.2 4.3 - - - +
11D VAL* 2.6 40.9 + - + +
14D ILE* 3.4 31.6 - - + -
21D LEU* 4.1 15.7 - - + -
22D ARG* 1.3 77.1 - - - +
24D GLU* 1.3 64.0 + - - +
25D VAL* 3.7 24.7 - - + -
36D TRP 3.8 3.8 - - - +
37D SER* 4.3 20.2 - - - +
502D VAL* 5.1 4.5 - - + -
506D LEU* 3.9 17.0 - - + -
520D ILE* 4.0 12.8 - - + -
524D VAL* 3.7 21.1 - - + -
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Residues in contact with GLU 24 (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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8D LYS* 4.6 13.0 - - + +
9D ILE 3.4 5.8 - - - +
10D VAL* 4.2 10.3 - - + +
22D ARG* 2.7 37.5 + - - +
23D ILE* 1.3 76.9 - - - +
25D VAL* 1.3 64.2 - - - +
36D TRP* 3.0 46.6 + - + +
38D MET* 3.4 22.0 - - - +
348D PHE* 4.8 0.9 - - - -
349D HIS* 2.6 31.8 + - - -
196I ALA* 4.6 2.8 - - - +
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Residues in contact with VAL 25 (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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8D LYS* 2.9 12.5 - - - +
9D ILE* 2.8 63.8 + - + +
23D ILE* 3.7 20.4 - - + -
24D GLU* 1.3 79.5 - - - +
26D GLU* 1.3 59.4 + - - +
27D VAL* 3.8 14.8 - - + -
32D ILE* 4.1 13.7 - - + -
34D ASN 3.5 8.3 - - - +
35D ALA* 4.0 6.5 - - + -
36D TRP* 4.2 2.2 - - - -
506D LEU* 4.0 16.8 - - + -
520D ILE* 3.8 18.2 - - + -
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Residues in contact with GLU 26 (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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7D ASN 3.3 7.4 - - - +
8D LYS* 3.1 31.6 + - - +
25D VAL* 1.3 73.6 - - - +
27D VAL* 1.3 58.6 + - - +
32D ILE* 3.5 3.3 - - - -
33D LYS* 2.7 71.9 + - + +
34D ASN* 3.2 19.6 + - + +
36D TRP* 3.7 20.7 - - + -
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Residues in contact with VAL 27 (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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7D ASN 2.7 28.8 + - - +
9D ILE* 3.8 31.4 - - + -
25D VAL* 3.8 14.6 - - + -
26D GLU* 1.3 82.9 - - - +
28D GLU* 1.3 65.4 + - - +
30D GLY* 3.8 13.5 - - - +
31D LYS 3.4 24.2 - - - +
32D ILE* 4.5 6.7 - - - -
33D LYS* 4.8 0.7 - - - +
511D ILE* 4.5 13.9 - - + -
514D PRO* 6.2 2.9 - - + -
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Residues in contact with GLU 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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27D VAL* 1.3 77.2 - - - +
29D GLY* 1.3 66.8 + - - +
31D LYS* 3.1 20.9 + - + +
33D LYS* 3.6 40.5 - - + +
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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