Contacts of the strand formed by residues 96 - 102 (chain o) in PDB entry 5GJQ
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 96 (chain o).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46o SER 3.6 4.7 - - - -
51o ASP* 4.8 8.7 - - + -
52o THR* 3.9 20.2 - - + -
55o VAL* 5.3 2.5 - - + -
87o CYS* 4.1 22.4 - - - -
94o LEU* 3.8 5.4 + - + -
95o MET* 1.3 77.0 - - - +
97o GLY* 1.3 57.7 + - - +
98o ILE* 4.0 11.2 - - + +
114o VAL 4.0 2.1 - - - +
115o PRO 3.8 3.5 - - - +
116o MET* 3.3 29.5 + - - +
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Residues in contact with GLY 97 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3o ILE* 3.7 4.9 - - - +
44o CYS 3.7 2.4 - - - +
46o SER* 2.5 52.3 + - - -
47o GLY* 4.8 1.0 - - - -
96o ALA* 1.3 70.5 - - - +
98o ILE* 1.3 59.9 + - - +
114o VAL 3.8 4.5 - - - -
115o PRO* 4.5 8.1 - - - -
116o MET* 4.6 4.6 - - - +
35u ARG* 5.8 3.6 - - - -
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Residues in contact with ILE 98 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43o CYS* 4.4 6.3 - - + -
44o CYS 3.4 5.6 - - - +
45o ARG* 4.1 14.1 - - + -
52o THR* 3.9 29.2 - - + +
55o VAL* 5.9 1.1 - - + -
83o PHE* 3.9 27.8 - - + -
87o CYS* 4.7 7.6 - - - -
96o ALA* 4.0 15.7 - - + +
97o GLY* 1.3 81.5 - - - +
99o ILE* 1.3 70.7 + - - +
100o ILE* 3.5 25.6 - - + -
113o SER* 3.8 0.7 - - - -
114o VAL* 2.9 45.3 + - + +
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Residues in contact with ILE 99 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3o ILE* 3.9 31.9 - - + +
4o MET* 4.4 4.3 - - - +
5o ALA* 3.8 23.6 - - + -
43o CYS* 3.3 2.3 - - - -
44o CYS* 2.8 47.3 + - + -
98o ILE* 1.3 78.7 - - - +
100o ILE* 1.3 63.8 + - - +
101o ALA* 3.7 1.2 + - + -
111o VAL* 4.0 9.9 - - + -
112o TYR 3.4 13.0 - - - +
113o SER* 4.2 9.9 - - - +
126o ALA* 3.7 33.0 - - + +
127o ILE* 4.0 8.7 - - - +
128o GLY* 5.5 0.4 - - - -
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Residues in contact with ILE 100 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41o ILE* 4.1 13.2 - - + -
42o PHE 3.6 7.6 - - - +
43o CYS* 4.2 5.4 - - + +
76o VAL* 4.0 20.0 - - + +
79o ALA* 4.2 0.4 - - + -
80o ALA* 4.0 27.4 - - + +
83o PHE* 3.5 43.3 - - + -
98o ILE* 3.5 22.0 - - + -
99o ILE* 1.3 73.4 - - - +
101o ALA* 1.3 62.1 + - - +
111o VAL* 3.6 0.3 - - - -
112o TYR* 2.8 38.1 + - - +
114o VAL* 3.9 17.5 - - + -
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Residues in contact with ALA 101 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5o ALA* 4.4 2.9 - - + -
12o VAL* 4.1 4.0 - - + -
14o LEU* 3.4 33.9 - - + -
41o ILE* 4.7 0.7 - - - -
42o PHE* 2.9 37.3 + - - +
76o VAL* 4.4 4.0 - - - -
99o ILE* 3.7 3.0 + - + -
100o ILE* 1.3 77.2 - - - +
102o GLY* 1.3 59.3 + - - +
110o GLN 3.2 11.7 - - - +
111o VAL* 3.7 15.3 - - + -
179o ILE* 3.8 1.7 - - - +
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Residues in contact with GLY 102 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12o VAL* 3.7 15.4 - - - +
40o ARG 3.2 12.3 - - - -
41o ILE* 4.3 1.3 - - - -
76o VAL* 3.5 15.5 - - - +
101o ALA* 1.3 76.8 - - - +
103o TRP* 1.3 60.4 - - - -
109o GLY* 3.5 3.0 - - - -
110o GLN 2.9 32.6 + - - +
179o ILE* 4.3 3.4 - - - -
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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