Contacts of the strand formed by residues 141 - 148 (chain B) in PDB entry 1GGT
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 SER 141 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85B GLN* 3.8 20.0 + - - -
86B ILE 3.3 3.6 - - - -
87B ASP* 2.5 32.8 + - - -
136B MET* 3.8 6.7 - - - +
137B ARG* 3.2 2.6 - - - -
138B GLU* 2.7 35.0 + - - -
139B ASP 3.1 10.4 + - - -
140B ARG* 1.3 77.6 - - - +
142B VAL* 1.3 63.3 + - - +
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Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B GLN* 3.3 3.8 - - - -
86B ILE* 2.9 40.3 + - + +
88B PHE* 3.7 19.3 - - + -
92B TYR* 3.9 35.0 - - + -
99B PHE* 3.9 17.0 - - + -
134B ILE* 4.0 13.7 - - + -
136B MET 3.6 3.8 - - - -
137B ARG* 3.8 19.7 - - + -
140B ARG 4.1 0.4 + - - -
141B SER* 1.3 74.6 - - - +
143B ARG* 1.3 60.1 + - - +
144B LEU* 3.9 11.4 + - + +
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Residues in contact with ARG 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B PHE* 3.6 33.5 - - - -
83B TYR* 4.4 11.0 - - + -
84B VAL 3.4 6.3 - - - +
85B GLN* 2.7 32.7 + - - +
134B ILE* 3.7 1.4 - - - -
135B VAL* 2.8 48.3 + - + +
136B MET* 2.9 42.1 + - + +
141B SER 4.1 0.6 + - - -
142B VAL* 1.3 71.4 - - - +
144B LEU* 1.3 64.4 + - - +
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Residues in contact with LEU 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B TYR* 3.3 12.9 - - - -
84B VAL* 2.8 45.8 + - + +
86B ILE* 3.5 33.0 - - + -
99B PHE* 4.4 12.6 - - + -
101B VAL* 4.5 11.2 - - + -
121B ILE* 3.9 16.6 - - + -
132B ALA* 4.8 2.9 - - + -
133B LYS 2.9 22.4 - - - +
134B ILE* 3.8 24.5 - - + -
135B VAL* 4.6 0.9 - - - -
142B VAL* 4.4 8.5 - - + -
143B ARG* 1.3 76.1 - - - +
145B SER* 1.3 61.5 + - - +
146B ILE* 3.8 8.5 - - + -
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Residues in contact with SER 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B SER* 3.9 19.1 + - - -
82B PHE 3.4 7.0 - - - -
83B TYR* 3.8 23.6 + - - -
125B LEU* 3.6 17.0 - - - +
132B ALA* 3.6 3.1 - - - -
133B LYS* 3.1 33.0 + - - -
135B VAL* 4.5 12.1 - - - -
144B LEU* 1.3 72.6 - - - +
146B ILE* 1.3 61.1 + - - +
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Residues in contact with ILE 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B SER* 3.1 4.2 - - - -
82B PHE* 3.0 48.2 + - + +
84B VAL* 4.0 25.6 - - + -
101B VAL* 4.0 27.1 - - + -
103B TYR* 3.7 24.2 - - + +
119B VAL* 3.6 15.3 - - + -
130B TRP* 3.7 13.7 - - + -
131B GLY 3.4 12.6 - - - +
132B ALA* 4.3 11.7 - - + +
144B LEU* 4.5 3.4 - - + -
145B SER* 1.3 73.5 - - - +
147B GLN* 1.3 69.9 + - - +
159B MET* 4.3 1.1 - - + -
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Residues in contact with GLN 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B GLY 4.5 8.1 - - - +
80B GLN* 4.4 12.0 - - - +
81B SER* 4.1 13.4 + - - +
82B PHE* 4.9 0.2 - - - -
125B LEU* 3.9 29.2 - - + +
126B GLN 2.9 34.1 + - - +
127B SER* 5.0 0.2 - - - +
128B GLY* 4.3 8.1 - - - +
129B LYS 3.8 10.5 + - - +
130B TRP* 2.9 20.9 - - - -
131B GLY 2.9 18.2 + - - -
145B SER 3.8 0.6 + - - -
146B ILE* 1.3 76.1 - - - +
148B SER* 1.3 72.2 + - - +
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Residues in contact with SER 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B VAL* 5.4 1.6 - - - +
77B ARG 4.0 1.6 + - - -
78B ARG* 3.5 11.9 - - - -
79B GLY* 3.3 26.2 + - - -
80B GLN 3.4 12.5 + - - -
82B PHE* 4.6 6.4 - - - -
128B GLY* 4.8 0.5 - - - -
129B LYS 4.6 2.4 + - - +
130B TRP* 3.6 32.1 - - - -
147B GLN* 1.3 90.0 + - - +
149B SER* 1.3 64.4 + - - +
150B PRO* 3.8 2.1 - - - +
152B CYS* 4.8 1.3 - - - -
182B ILE* 4.8 9.0 - - - +
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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