Contacts of the strand formed by residues 51 - 60 (chain D) in PDB entry 5IRC
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 LYS 51 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46D ILE 3.6 1.4 - - - +
47D GLU* 3.2 5.6 - - - +
48D VAL* 3.0 35.1 + - - +
49D ASP* 3.7 29.3 + - - +
50D GLY* 1.3 82.3 - - - +
52D GLN* 1.3 63.8 + - - +
53D VAL* 3.6 7.2 + - + +
179D LEU* 4.4 31.6 - - + +
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Residues in contact with GLN 52 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4D ILE* 3.2 22.9 + - - +
45D ASP* 5.4 9.2 - - + -
46D ILE 3.7 8.5 - - - +
47D GLU* 4.3 14.5 + - + +
50D GLY 4.1 1.4 + - - -
51D LYS* 1.3 72.6 - - - +
53D VAL* 1.3 66.9 + - - +
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Residues in contact with VAL 53 (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 ILE* 3.3 17.3 - - + +
6D LYS* 4.1 24.0 - - + -
44D ALA 3.5 1.2 - - - +
45D ASP* 3.5 2.8 - - - -
46D ILE* 2.7 39.5 + - + +
48D VAL* 4.7 0.2 - - + -
51D LYS* 3.8 13.2 - - + +
52D GLN* 1.3 82.2 - - - +
54D GLU* 1.3 65.4 + - - +
55D LEU* 3.4 9.9 + - + +
175D THR* 3.7 31.0 - - + -
179D LEU* 4.0 23.6 - - + -
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Residues in contact with GLU 54 (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 ILE 2.8 13.6 + - - +
5D ARG* 3.4 21.0 - - + +
6D LYS 3.1 21.8 + - - +
43D VAL* 4.8 10.3 - - + -
44D ALA 3.8 3.8 - - - -
45D ASP* 4.4 11.7 - - - +
52D GLN 4.3 0.2 - - - -
53D VAL* 1.3 70.1 - - - +
55D LEU* 1.3 61.6 + - - +
56D ALA* 3.6 1.0 + - - +
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Residues in contact with LEU 55 (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 LYS* 3.4 33.2 - - + +
7D LYS 4.6 0.7 - - - -
8D LEU* 4.0 28.0 - - + +
43D VAL* 3.3 6.6 - - - -
44D ALA* 2.8 46.0 + - + +
46D ILE* 4.7 5.8 - - + -
53D VAL* 3.4 10.7 + - + +
54D GLU* 1.3 71.1 - - - +
56D ALA* 1.3 63.3 + - - +
57D LEU* 3.6 24.5 + - + +
79D VAL* 4.9 5.4 - - + -
171D PHE* 4.3 12.6 - - + +
175D THR* 3.5 26.2 - - - +
178D ALA* 5.0 3.1 - - + -
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Residues in contact with ALA 56 (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 LYS 2.7 17.4 + - - +
7D LYS* 4.1 6.5 - - + -
8D LEU* 2.7 35.5 + - - +
42D TYR 3.7 6.1 - - - +
43D VAL* 4.4 8.7 - - + -
54D GLU 3.6 2.4 + - - +
55D LEU* 1.3 71.8 - - - +
57D LEU* 1.3 58.4 + - - +
58D TRP* 3.8 20.4 - - - +
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Residues in contact with LEU 57 (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 LEU* 3.7 18.2 - - + -
22D LEU* 4.2 37.7 - - + +
25D ASN* 4.5 4.3 - - - +
41D ASN* 3.3 4.2 - - - -
42D TYR* 2.7 60.5 + - + +
43D VAL 4.4 0.7 - - - -
44D ALA* 4.1 21.3 - - + +
55D LEU* 3.8 39.7 - - + +
56D ALA* 1.3 72.3 - - - +
58D TRP* 1.3 64.4 + - - +
59D ASP 3.6 1.4 + - - -
171D PHE* 4.1 13.5 - - + -
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Residues in contact with TRP 58 (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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1412B MET* 6.0 0.9 - - - -
7D LYS* 3.4 50.2 - - + +
8D LEU* 2.8 23.0 + - - +
9D VAL* 3.6 14.5 - - + +
10D ILE* 3.1 28.5 + - - +
22D LEU* 4.7 0.2 - - - -
39D PHE* 3.8 19.1 - + - -
41D ASN* 3.6 34.1 - - - +
56D ALA* 3.8 19.5 - - + +
57D LEU* 1.3 74.1 - - - +
59D ASP* 1.3 60.7 + - - +
60D THR* 4.0 0.4 + - - -
72D LEU 4.2 6.1 - - - -
73D SER* 3.8 28.7 - - - +
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Residues in contact with ASP 59 (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 ILE* 3.6 14.8 - - - +
18D LYS* 4.1 6.6 - - - +
19D THR* 2.5 40.6 + - - +
22D LEU* 3.6 19.3 - - + +
37D THR* 3.6 14.9 + - + +
39D PHE* 3.9 6.4 - - - -
40D GLU* 2.8 39.6 + - + +
41D ASN* 5.0 0.2 - - - +
42D TYR* 4.0 8.4 + - + -
57D LEU 3.6 1.6 + - - -
58D TRP* 1.3 72.2 - - - +
60D THR* 1.3 76.5 + - - +
73D SER* 4.6 4.5 + - - -
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Residues in contact with THR 60 (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 VAL* 4.0 17.7 - - + -
10D ILE 2.7 27.2 + - - +
11D VAL* 3.8 12.2 - - + +
18D LYS* 3.5 19.1 - - - -
37D THR* 4.0 11.6 - - - -
38D VAL 4.3 6.5 - - - -
39D PHE* 6.2 0.4 - - - -
58D TRP 4.1 1.3 - - - +
59D ASP* 1.3 89.6 + - - +
61D ALA* 1.3 60.8 + - - +
62D GLY 3.9 0.2 + - - -
70D ARG* 4.0 24.5 - - + -
73D SER* 3.9 21.5 - - - +
203D MGF 4.0 1.0 - - - -
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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