Contacts of the strand formed by residues 92 - 99 (chain X) in PDB entry 3HI6
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 92 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38X ARG* 3.9 15.7 - - + -
39X GLN 3.3 30.5 - - - +
40X ALA* 3.6 5.4 - - + +
41X PRO* 4.8 2.0 - - - -
89X GLU 5.7 0.2 - - - +
90X ASP 3.1 10.4 + - - +
91X THR* 1.3 77.6 - - - +
93X VAL* 1.3 62.2 + - - +
94X TYR* 3.4 8.5 - - + -
115X MET* 3.9 9.0 - - - -
116X VAL 3.0 29.2 + - - +
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Residues in contact with VAL 93 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37X VAL 4.0 0.2 - - - +
38X ARG* 3.1 5.7 - - - +
39X GLN* 2.8 39.5 + - + +
92X ALA* 1.3 71.5 - - - +
94X TYR* 1.3 63.0 + - - +
95X TYR* 3.5 37.6 + - + +
112X GLN 5.2 0.4 - - - +
113X GLY* 3.8 18.6 - - - -
114X THR 3.6 8.1 - - - +
115X MET* 3.4 32.1 - - + +
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Residues in contact with TYR 94 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6X GLU* 3.7 3.8 - - - +
20X LEU* 3.6 28.7 - - + -
36X TRP* 4.4 6.7 - + + -
37X VAL 3.7 2.9 - - - -
38X ARG* 3.1 41.6 + - + -
48X VAL* 4.7 6.1 - - + -
68X PHE* 3.9 12.7 - + - -
81X LEU* 4.2 9.4 - - + -
83X MET* 3.9 15.9 - - - -
90X ASP* 2.7 34.5 + - - +
92X ALA* 3.4 20.6 - - + -
93X VAL* 1.3 74.0 - - - +
95X TYR* 1.3 61.9 + - - +
113X GLY* 3.4 1.9 - - - -
114X THR* 2.8 42.5 + - + +
116X VAL* 3.5 22.9 - - + -
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Residues in contact with TYR 95 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6X GLU* 3.1 5.4 - - - +
36X TRP* 3.2 9.6 - - - -
37X VAL 2.7 47.2 + - - +
38X ARG* 5.0 0.4 - - - -
39X GLN* 4.0 18.6 + - + -
45X LEU* 4.4 11.0 - - + -
93X VAL* 3.5 31.5 - - + +
94X TYR* 1.3 73.4 - - - +
96X CYS* 1.3 59.6 + - - +
110X TRP* 3.7 30.1 - + + -
111X GLY 3.7 14.1 - - - -
112X GLN 3.7 5.4 + - - -
113X GLY* 3.5 22.4 - - - -
38Y GLN* 3.4 7.5 + - - -
41Y GLY 5.4 0.7 - - - -
42Y LYS 3.3 19.9 + - - -
43Y ALA* 3.7 26.5 - - + -
44Y PRO* 4.3 0.9 - - + -
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Residues in contact with CYS 96 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4X LEU* 3.7 14.4 - - - -
6X GLU* 2.9 22.8 + - - -
22X CYS* 2.1 54.1 - - + -
34X MET* 4.8 1.1 - - + -
35X TRP 3.1 11.4 - - - +
36X TRP* 3.9 6.8 - - + -
79X LEU* 3.9 10.5 - - + -
95X TYR* 1.3 75.6 - - - +
97X ALA* 1.3 64.3 + - - +
110X TRP* 3.5 1.6 - - - -
111X GLY 2.9 25.5 + - - -
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Residues in contact with ALA 97 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4X LEU* 4.0 1.8 - - - -
34X MET* 3.5 9.1 - - - +
35X TRP* 2.7 41.5 + - + -
37X VAL* 4.7 1.8 - - + -
95X TYR 4.3 0.2 + - - -
96X CYS* 1.3 77.9 - - - +
98X SER* 1.3 61.0 + - - +
107X PHE* 3.7 28.3 - - + -
109X ILE 3.1 13.9 - - - +
110X TRP* 4.1 21.1 - - + -
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Residues in contact with SER 98 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4X LEU* 4.1 1.2 - - - +
27X PHE* 4.4 11.4 - - - -
32X TYR* 4.1 15.9 - - - -
33X VAL 3.7 4.5 - - - -
34X MET* 3.8 18.6 - - - -
35X TRP* 4.2 3.1 - - - -
97X ALA* 1.3 75.6 - - - +
99X SER* 1.3 60.0 + - - +
107X PHE* 3.4 8.0 - - - +
108X ASP* 2.8 31.5 + - - +
109X ILE* 3.0 36.5 + - - +
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Residues in contact with SER 99 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32X TYR* 3.1 26.0 - - - -
33X VAL* 3.0 21.2 + - - +
35X TRP* 3.0 21.2 + - - +
98X SER* 1.3 71.9 - - - +
100X TYR* 1.3 64.9 + - - +
102X PHE 3.2 26.5 + - - -
103X TRP* 3.7 1.5 - - - -
104X SER 2.7 24.8 + - - -
106X ALA 3.6 4.5 - - - -
108X ASP* 4.0 2.0 - - - +
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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