Contacts of the strand formed by residues 98 - 105 (chain s) 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 GLY 98 (chain s).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44s THR* 3.9 3.1 + - - -
46s ALA* 2.8 41.6 + - - +
52s CYS* 4.2 0.9 - - - -
97s MET* 1.3 74.9 - - - +
99s THR* 1.3 60.7 + - - -
113s TYR* 4.2 2.0 - - - -
114s VAL 3.6 4.7 - - - -
115s ASP* 4.1 8.7 - - - -
128s VAL* 3.7 21.0 - - - +
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Residues in contact with THR 99 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43s GLY* 4.0 0.2 - - - -
44s THR* 2.9 20.6 + - - -
52s CYS* 5.2 0.9 - - - -
56s GLU* 2.4 31.1 + - - +
83s LEU* 3.6 14.8 - - + -
97s MET* 3.6 23.1 - - + -
98s GLY* 1.3 73.7 - - - -
100s MET* 1.3 71.7 + - - +
101s ILE* 4.0 3.5 - - + +
112s TYR 3.7 0.2 - - - +
113s TYR* 3.5 7.1 - - - -
114s VAL* 2.8 47.3 + - + +
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Residues in contact with MET 100 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3s THR* 3.3 27.4 - - - +
4s LEU* 3.7 22.4 - - - +
5s ALA* 3.5 19.3 - - + -
42s LEU 3.4 1.7 - - - +
43s GLY* 3.2 22.3 - - - -
44s THR* 2.9 28.2 + - + +
99s THR* 1.3 80.8 + - - +
101s ILE* 1.3 64.4 + - - +
102s CYS* 3.7 6.6 - - - -
111s LEU* 4.2 11.0 - - + -
112s TYR 3.2 7.2 - - - +
113s TYR* 4.4 4.5 - - + -
126s PHE* 3.5 32.8 - - + +
128s VAL* 4.0 15.0 - - + -
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Residues in contact with ILE 101 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37s ILE* 4.0 22.2 - - + -
41s LEU* 4.2 23.3 - - + -
42s LEU 3.3 5.2 - - - +
43s GLY* 4.1 1.1 - - - -
56s GLU* 4.2 1.3 - - - +
59s LEU* 4.2 3.8 - - + -
76s VAL* 3.8 13.0 - - + +
79s ALA* 4.3 15.7 - - + -
80s SER* 4.2 27.1 - - - -
83s LEU* 4.0 25.8 - - + -
99s THR* 4.0 10.1 - - + +
100s MET* 1.3 76.4 - - - +
102s CYS* 1.3 59.4 + - - +
110s GLY 3.8 0.7 - - - +
111s LEU* 3.4 2.4 - - - -
112s TYR* 2.8 39.8 + - + +
114s VAL* 4.6 4.0 - - + -
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Residues in contact with CYS 102 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5s ALA* 4.3 2.2 - - - -
12s VAL* 3.8 18.2 - - + -
14s VAL* 3.6 30.3 - - + -
41s LEU* 3.7 5.4 - - - +
42s LEU* 2.9 35.0 + - + +
76s VAL* 4.7 0.2 - - - -
100s MET* 3.7 16.4 - - - -
101s ILE* 1.3 73.7 - - - +
103s GLY* 1.3 58.8 + - - +
110s GLY 3.3 6.1 - - - -
111s LEU* 3.4 26.7 - - - -
179s VAL* 4.2 9.3 - - + +
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Residues in contact with GLY 103 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12s VAL* 4.1 2.2 - - - +
40s TYR 4.0 11.7 - - - -
41s LEU* 4.3 2.0 - - - -
76s VAL* 3.7 18.3 - - - +
102s CYS* 1.3 75.8 - - - +
104s TRP* 1.3 60.9 + - - +
109s PRO* 3.4 4.3 - - - +
110s GLY 2.9 28.3 + - - +
179s VAL* 3.8 17.6 - - - +
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Residues in contact with TRP 104 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9s ARG 4.2 7.4 - - - -
10s HIS* 3.9 6.5 - - - -
11s GLY* 3.3 32.8 - - - -
40s TYR* 4.5 9.4 + - - +
73s ARG* 6.0 0.2 + - - -
74s ILE 5.8 0.3 - - - +
76s VAL* 4.0 3.6 - - - +
103s GLY* 1.3 72.1 - - - -
105s ASP* 1.3 86.2 + - - +
108s GLY* 3.6 18.9 - - - -
109s PRO* 3.7 24.7 - - + -
179s VAL* 3.8 9.5 - - + +
180s ARG* 3.2 22.7 - - - +
181s GLU* 3.1 70.3 + - + +
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Residues in contact with ASP 105 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100k ASP* 5.4 0.7 - - - +
75s SER* 3.1 37.6 - - - +
76s VAL* 3.3 18.0 + - + +
77s ALA 4.4 0.3 + - - -
104s TRP* 1.3 82.4 - - - +
106s LYS* 1.3 83.2 + - - +
107s ARG* 3.1 27.4 + - + +
108s GLY* 2.9 32.2 + - - +
110s GLY* 5.9 0.2 - - - -
181s GLU* 5.6 0.3 - - - +
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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