Contacts of the strand formed by residues 91 - 100 (chain D) in PDB entry 4X7C
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 ALA 91 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38D ARG* 3.8 31.4 - - + -
39D GLN 3.8 16.2 - - - -
40D ALA* 3.9 7.6 - - + +
41D PRO* 5.8 1.3 - - - -
89D ASP 3.1 4.3 + - - +
90D THR* 1.3 77.9 - - - +
92D VAL* 1.3 58.3 + - - +
93D TYR* 3.4 11.3 - - + -
115D GLN* 3.6 10.1 - - - +
116D VAL 2.7 35.7 + - - +
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Residues in contact with VAL 92 (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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37D TYR 3.9 0.2 - - - +
38D ARG* 3.1 4.5 - - - -
39D GLN* 2.9 40.7 + - + +
40D ALA* 4.9 0.2 - - - +
41D PRO* 5.8 6.5 - - + -
91D ALA* 1.3 74.3 - - - +
93D TYR* 1.3 62.6 + - - +
94D TYR* 4.0 9.1 + - + +
110D ARG* 5.7 1.3 - - - +
112D ARG 4.6 3.8 - - - +
113D GLY* 4.0 24.7 - - - -
114D THR 3.6 8.5 - - - +
115D GLN* 3.4 24.2 - - + +
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Residues in contact with TYR 93 (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 GLU* 3.8 2.3 - - - +
20D LEU* 3.8 28.3 - - + -
36D TRP* 4.6 7.2 - - + -
37D TYR 3.4 4.9 - - - +
38D ARG* 2.8 39.5 + - + -
48D VAL* 3.9 15.9 - - + -
67D PHE* 4.1 6.5 - + - -
80D LEU* 4.6 5.6 - - + -
82D MET* 3.5 22.1 - - + +
89D ASP* 2.7 36.5 + - - +
91D ALA* 3.4 19.3 - - + -
92D VAL* 1.3 73.6 - - - +
94D TYR* 1.3 60.6 + - - +
113D GLY* 3.2 1.3 - - - -
114D THR* 2.9 35.8 + - - +
116D VAL* 3.5 25.4 - - + -
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Residues in contact with TYR 94 (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 GLU* 3.4 2.5 - - - -
36D TRP* 3.4 5.1 - - - -
37D TYR* 2.8 63.7 + - + +
38D ARG 4.4 2.0 - - - -
39D GLN* 4.4 22.8 + - + -
45D ARG* 3.3 35.2 + - - +
92D VAL* 4.3 11.0 - - + -
93D TYR* 1.3 75.9 - - - +
95D CYS* 1.3 72.8 + - - +
96D LYS* 3.7 15.4 + - - -
110D ARG* 3.6 53.1 + - + +
111D GLY 3.8 4.7 - - - +
113D GLY* 3.7 11.7 - - - -
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Residues in contact with CYS 95 (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 LEU* 4.0 7.6 - - + -
6D GLU* 2.9 19.5 + - + +
22D CYS* 2.0 56.1 - - + -
34D MET* 3.8 14.6 - - - -
35D GLY 3.3 10.1 - - - -
36D TRP* 3.7 13.9 - - + -
78D VAL* 4.8 1.6 - - - -
94D TYR* 1.3 74.8 - - - +
96D LYS* 1.3 64.2 + - - +
110D ARG* 3.2 5.0 - - - +
111D GLY 2.8 25.1 + - - +
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Residues in contact with LYS 96 (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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524B PHE* 3.7 21.0 - - + -
4D LEU* 4.1 3.8 - - - -
34D MET* 3.4 4.9 - - - +
35D GLY 2.7 37.2 + - - +
37D TYR* 3.5 34.3 - - + -
45D ARG* 3.5 28.3 - - - +
94D TYR* 4.4 12.0 - - + +
95D CYS* 1.3 77.4 - - - +
97D ARG* 1.3 66.1 + - - +
98D GLU* 4.5 19.2 + - - +
108D GLY* 6.1 2.1 - - - -
110D ARG* 4.3 20.2 - - + +
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Residues in contact with ARG 97 (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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2D VAL* 4.3 6.3 - - + -
4D LEU* 3.9 20.4 - - + +
24D ALA* 3.7 25.1 - - - +
28D ILE* 3.6 22.6 - - - +
29D PHE 3.3 17.8 + - - -
32D TYR* 3.4 27.5 - - - -
33D ALA 3.4 5.2 - - - +
34D MET* 3.4 38.0 - - + +
76D ASN* 4.9 12.9 + - - +
96D LYS* 1.3 78.9 - - - +
98D GLU* 1.3 67.4 + - - +
99D ASP* 2.8 39.2 + - - +
107D SER 3.7 1.3 - - - +
108D GLY* 3.3 27.4 - - - -
110D ARG 4.9 1.6 - - - +
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Residues in contact with GLU 98 (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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522B ASN* 2.9 23.0 + - - -
523B GLN* 6.3 0.2 - - - -
524B PHE* 3.4 28.3 - - + -
32D TYR* 3.2 9.2 - - - +
33D ALA 2.9 30.0 + - - -
96D LYS* 4.5 17.2 + - + +
97D ARG* 1.3 75.4 - - - +
99D ASP* 1.3 61.4 + - - +
100D TYR* 3.3 26.8 - - + +
106D PRO* 3.7 11.8 - - + +
107D SER 3.5 1.6 - - - -
108D GLY* 3.5 22.8 + - - -
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Residues in contact with ASP 99 (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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2D VAL* 3.7 16.3 - - + +
27D SER 4.7 0.7 - - - +
28D ILE* 3.4 6.2 - - - -
29D PHE* 2.7 49.3 + - + +
31D ILE 4.1 1.6 - - - -
32D TYR* 4.0 0.7 - - - +
97D ARG* 2.8 45.2 + - - +
98D GLU* 1.3 71.8 - - - +
100D TYR* 1.3 61.0 + - - +
105D PRO 4.6 0.9 - - - +
106D PRO* 3.5 3.5 - - - +
107D SER* 2.9 42.6 + - - +
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Residues in contact with TYR 100 (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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519B SER* 3.7 15.8 + - - -
520B TRP 3.3 22.4 - - - +
521B VAL* 3.5 21.3 - - + -
522B ASN* 2.7 31.2 + - - -
524B PHE* 3.5 3.1 - - - +
525B TYR* 3.5 27.8 + + + -
29D PHE* 3.4 21.4 - - - +
31D ILE* 3.0 18.4 + - + +
32D TYR* 3.5 22.9 - - - -
33D ALA* 3.6 21.8 - - - +
98D GLU* 3.3 20.6 - - + +
99D ASP* 1.3 75.0 - - - +
101D SER* 1.3 62.5 + - - +
106D PRO* 3.7 24.2 - - + -
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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