Contacts of the strand formed by residues 64 - 70 (chain D) in PDB entry 2R7I
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 64 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55D GLU* 5.2 8.1 - - + -
56D ALA 3.6 4.9 - - - +
57D ILE* 4.4 14.8 - - + -
62D ASN 4.6 7.6 - - - +
63D GLU* 1.3 80.0 - - - +
65D VAL* 1.3 64.4 + - - +
114D GLU* 5.2 0.3 - - - -
115D HIS* 3.1 51.0 + - + +
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Residues in contact with VAL 65 (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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39D TYR* 4.0 18.2 - - + -
55D GLU* 3.6 8.1 - - - +
56D ALA* 2.7 57.1 + - + +
57D ILE* 4.2 1.1 - - - +
58D ASN* 5.0 3.4 - - + +
63D GLU* 3.7 24.2 - - + +
64D LYS* 1.3 80.8 - - - +
66D VAL* 1.3 64.7 + - - +
67D VAL* 4.1 1.8 - - + -
98D ALA* 5.5 4.5 - - + -
112D VAL* 3.9 24.5 - - + -
113D PHE 3.4 15.9 - - - +
114D GLU* 5.5 1.3 - - - -
115D HIS* 4.1 5.3 - - - +
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Residues in contact with VAL 66 (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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45D LEU* 5.3 6.7 - - + -
53D VAL* 4.2 21.8 - - + -
54D PHE 3.3 11.7 - - - +
55D GLU* 4.8 4.5 - - + -
65D VAL* 1.3 79.6 - - - +
67D VAL* 1.3 66.9 + - - +
68D LYS* 4.8 2.0 - - + +
111D LEU 3.8 1.2 - - - +
112D VAL* 3.4 1.4 - - - -
113D PHE* 2.7 54.7 + - + +
114D GLU 4.9 2.2 - - - +
115D HIS* 4.7 21.0 - - + +
116D VAL 4.9 7.4 - - - +
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Residues in contact with VAL 67 (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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36D GLN* 4.4 11.2 - - - +
39D TYR* 4.5 9.6 - - + -
41D LEU* 4.4 15.9 - - + -
53D VAL* 3.4 2.1 - - - +
54D PHE* 2.8 43.0 + - + +
56D ALA* 3.6 25.1 - - + -
65D VAL* 4.1 9.6 + - + -
66D VAL* 1.3 77.5 - - - +
68D LYS* 1.3 62.1 + - - +
69D ILE* 3.9 11.1 + - + -
101D VAL* 5.2 0.9 - - + -
110D ALA* 4.0 22.9 - - + -
111D LEU 3.5 4.9 - - - +
112D VAL* 4.1 16.6 - - + -
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Residues in contact with LYS 68 (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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50D TYR* 5.0 2.7 - - - -
51D SER* 3.4 33.9 - - - -
52D GLU 3.6 4.7 - - - +
53D VAL* 4.2 13.9 - - + +
66D VAL* 4.0 2.4 + - + -
67D VAL* 1.3 71.3 - - - +
69D ILE* 1.3 61.9 + - - +
70D LEU* 3.3 18.7 + - + +
81D GLU* 2.9 31.1 + - - -
110D ALA* 4.1 0.9 - - - -
111D LEU* 2.8 37.9 + - + +
113D PHE* 4.2 24.7 - - + -
175D ASP* 3.5 28.9 + - - +
177D GLY* 5.0 1.4 - - - +
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Residues in contact with ILE 69 (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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36D GLN* 4.6 9.4 - - - +
41D LEU* 4.7 12.1 - - + -
51D SER* 3.3 3.8 - - - -
52D GLU* 3.0 37.6 + - + +
54D PHE* 3.4 34.5 - - + -
67D VAL* 3.8 6.9 - - + -
68D LYS* 1.3 68.4 - - - +
70D LEU* 1.3 74.7 + - - +
71D LYS* 4.9 0.7 - - - +
103D ASP* 5.3 5.8 - - - +
108D THR* 4.0 19.3 - - + +
109D PRO 4.0 2.9 - - - +
110D ALA* 3.7 16.6 - - + -
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Residues in contact with LEU 70 (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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50D TYR 4.2 8.1 - - - +
68D LYS* 3.8 40.6 - - + +
69D ILE* 1.3 77.6 - - - +
71D LYS* 1.3 66.1 + - - +
72D PRO* 4.6 0.2 - - - +
73D VAL* 5.7 0.4 - - + -
78D ILE* 3.6 42.6 - - + -
81D GLU* 4.2 12.6 - - - +
108D THR* 3.2 24.0 - - - +
109D PRO* 2.9 26.4 + - + +
111D LEU* 3.9 24.7 - - + -
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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