Contacts of the strand formed by residues 73 - 80 (chain D) in PDB entry 4LQL
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 VAL 73 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7D TYR* 4.2 1.3 - - - -
8D LYS 3.1 6.7 - - - -
10D TRP* 3.7 37.0 - - + +
67D ALA* 3.2 31.6 - - + +
70D ASN* 2.6 29.5 + - + +
71D ASP 3.1 2.8 - - - +
72D ASP* 1.3 67.5 - - - +
74D ALA* 1.3 67.9 + - - +
75D GLY 3.2 11.6 + - - +
98D LYS* 3.5 14.3 + - + +
171D ASN* 4.0 6.9 - - - -
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Residues in contact with ALA 74 (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 TYR* 3.8 18.6 - - + +
8D LYS 2.5 19.3 + - - +
9D PHE* 3.7 17.9 - - + -
46D TYR* 4.9 0.7 - - + -
72D ASP 3.0 3.8 + - - -
73D VAL* 1.3 72.5 - - - +
75D GLY* 1.3 56.7 + - - +
98D LYS* 5.2 0.2 - - - +
99D PRO* 3.9 3.6 - - - +
164D GLN 5.0 0.4 - - - +
167D ALA* 3.6 16.4 - - + +
168D VAL* 3.6 30.1 - - + +
171D ASN* 3.2 20.1 - - - -
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Residues in contact with GLY 75 (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 4.1 0.6 + - - -
9D PHE* 4.5 7.4 - - - -
10D TRP* 4.0 13.5 + - - +
73D VAL* 4.0 15.7 - - - +
74D ALA* 1.3 80.6 - - - +
76D VAL* 1.3 68.5 + - - +
98D LYS* 4.7 2.9 - - - -
99D PRO* 3.7 23.8 - - - -
163D TRP* 5.0 2.2 - - - -
167D ALA* 4.7 3.8 - - - +
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Residues in contact with VAL 76 (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 TRP* 3.9 11.2 - - + +
12D VAL* 6.3 2.7 - - + -
64D MET* 6.0 2.2 - - + -
67D ALA* 3.6 30.5 - - + -
75D GLY* 1.3 78.4 - - - +
77D ILE* 1.3 65.5 + - - +
96D LEU* 4.2 12.8 - - + -
98D LYS* 5.1 2.2 - - + -
99D PRO* 3.3 18.8 + - - +
100D LEU* 3.5 14.1 + - + -
101D LEU* 3.0 25.1 + - - +
163D TRP* 4.3 2.9 - - - -
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Residues in contact with ILE 77 (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 PHE* 4.7 14.6 - - + -
10D TRP 3.0 13.9 + - - +
11D PHE* 3.4 28.0 - - + -
12D VAL* 3.2 26.0 + - - +
48D VAL* 6.2 4.0 - - + -
76D VAL* 1.3 76.6 - - - +
78D THR* 1.3 59.0 + - - +
101D LEU* 3.8 28.9 - - + -
160D ILE* 6.0 3.6 - - + -
163D TRP* 4.2 15.3 - - + -
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Residues in contact with THR 78 (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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11D PHE* 5.0 0.2 - - - -
12D VAL* 4.0 12.1 - - - -
76D VAL* 4.1 1.2 + - - -
77D ILE* 1.3 73.7 - - - +
79D TRP* 1.3 55.6 + - - +
80D MET* 6.0 0.5 - - - +
89D TRP* 3.9 27.9 - - - -
100D LEU* 3.8 23.2 - - - +
101D LEU 2.7 31.7 + - - +
102D HIS* 3.3 12.0 - - - +
103D LEU* 2.8 20.9 + - - -
133D TYR* 5.0 5.7 - - - -
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Residues in contact with TRP 79 (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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11D PHE* 3.6 33.6 - + + -
12D VAL 3.2 17.9 + - - +
13D VAL* 3.5 13.6 - - + -
14D GLY 3.2 13.0 + - - -
31D ALA* 4.0 30.3 - - + -
34D LEU* 4.2 14.8 - - + -
77D ILE 4.1 0.4 + - - -
78D THR* 1.3 75.5 - - - +
80D MET* 1.3 88.3 + - - +
81D HIS* 3.3 47.3 - + - +
89D TRP* 5.2 1.9 - - - -
102D HIS* 6.1 0.7 - - - -
103D LEU* 3.1 31.0 - - + +
104D ALA* 4.9 0.4 - - - -
105D THR* 3.3 34.6 + - + +
106D GLN* 4.7 1.1 - - - -
107D PHE* 4.2 15.7 - - + -
126D SER* 4.4 0.4 - - - -
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Residues in contact with MET 80 (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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14D GLY 4.0 4.5 - - - +
78D THR* 5.8 1.3 - - - +
79D TRP* 1.3 104.0 + - - +
81D HIS* 1.3 56.9 + - - +
82D THR 3.8 9.6 - - - +
84D SER* 3.0 33.2 - - - +
89D TRP* 4.6 12.8 - - + -
102D HIS* 6.4 1.6 - - + -
103D LEU 4.6 0.6 + - - -
126D SER* 3.7 11.7 - - - +
129D GLY 4.2 11.0 - - - +
130D ASP* 4.9 7.7 - - + +
133D TYR* 4.2 23.3 - - + -
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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