Contacts of the strand formed by residues 141 - 148 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A GLN* 4.2 16.9 + - - -
86A ILE 3.3 4.5 - - - -
87A ASP* 2.8 29.2 + - - +
136A MET* 4.1 6.7 - - - +
137A ARG 2.7 33.6 - - - +
138A GLU 3.3 9.4 - - - +
139A ASP 2.7 12.0 + - - -
140A ARG* 1.3 74.1 - - - +
142A VAL* 1.3 61.4 + - - +
143A ARG 4.2 0.2 - - - -
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Residues in contact with VAL 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A GLN* 3.4 4.3 - - - +
86A ILE* 3.0 32.7 + - + +
88A PHE* 3.2 33.4 - - + -
92A TYR* 3.8 24.9 - - + -
99A PHE* 4.8 8.3 - - + -
134A ILE* 3.6 39.7 - - + -
136A MET 3.6 3.6 - - - +
137A ARG* 4.6 5.6 - - + +
140A ARG 4.8 0.2 - - - +
141A SER* 1.3 78.5 - - - +
143A ARG* 1.3 60.1 + - - +
144A LEU* 3.8 12.6 + - + -
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Residues in contact with ARG 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A PHE* 4.7 16.8 - - + -
83A TYR* 4.3 27.4 - - + -
84A VAL 3.4 13.7 - - - +
85A GLN* 4.2 18.4 + - + +
134A ILE* 4.1 0.3 - - - -
135A VAL* 2.8 56.4 + - - +
136A MET* 2.9 41.8 + - + +
141A SER 4.2 0.4 - - - -
142A VAL* 1.3 71.0 - - - +
144A LEU* 1.3 62.6 + - - +
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Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A TYR* 3.3 11.9 - - - -
84A VAL* 2.6 38.9 + - + +
86A ILE* 3.9 21.8 - - + -
99A PHE* 4.8 12.3 - - + -
101A VAL* 3.8 24.0 - - + -
121A ILE* 4.8 3.6 - - + -
132A ALA* 3.7 22.7 - - + -
133A LYS 3.4 15.0 - - - +
134A ILE* 3.8 26.7 - - + -
135A VAL* 4.6 0.4 - - - -
142A VAL* 3.8 11.6 + - + -
143A ARG* 1.3 75.2 - - - +
145A SER* 1.3 60.6 + - - +
146A ILE* 3.8 12.6 - - + -
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Residues in contact with SER 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A SER* 4.0 11.4 + - - -
82A PHE 3.7 5.8 + - - -
83A TYR* 3.7 16.0 + - - -
125A LEU* 3.6 24.7 - - - +
132A ALA* 3.5 1.0 - - - -
133A LYS* 2.9 33.3 + - - -
135A VAL* 3.5 25.6 - - - -
144A LEU* 1.3 71.1 - - - +
146A ILE* 1.3 61.7 + - - +
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Residues in contact with ILE 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A SER* 2.9 5.0 - - - -
82A PHE* 2.8 57.7 + - + +
84A VAL* 3.9 24.5 - - + -
101A VAL* 4.5 12.1 - - + -
103A TYR* 3.5 25.8 - - + +
119A VAL* 4.3 10.5 - - + -
130A TRP* 3.9 24.9 - - + -
131A GLY 3.9 2.9 - - - -
132A ALA* 3.8 16.6 - - + +
144A LEU* 4.4 9.2 - - + -
145A SER* 1.3 72.0 - - - +
147A GLN* 1.3 64.5 + - - +
159A MET* 4.2 9.2 - - + -
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Residues in contact with GLN 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A GLY* 4.1 14.4 + - - +
81A SER* 4.1 15.1 + - - +
125A LEU* 3.8 26.7 + - + +
126A GLN 3.1 29.4 + - - +
127A SER* 3.8 9.9 - - - +
128A GLY 3.9 5.5 - - - +
129A LYS 3.6 12.9 + - - +
130A TRP* 3.4 11.3 - - - -
131A GLY 3.0 32.4 + - - +
146A ILE* 1.3 80.5 - - - +
148A SER* 1.3 67.9 + - - +
150A PRO* 6.2 0.2 - - - +
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Residues in contact with SER 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A VAL* 5.2 1.7 - - - +
77A ARG 3.6 7.6 + - - -
78A ARG* 3.8 4.6 - - - -
79A GLY* 3.0 33.3 + - - -
80A GLN 3.4 19.5 + - - +
82A PHE* 4.6 8.7 - - - -
128A GLY 5.5 0.2 - - - -
129A LYS 4.7 1.3 - - - +
130A TRP* 3.9 27.8 - - - -
146A ILE* 4.3 0.8 - - - +
147A GLN* 1.3 84.2 + - - +
149A SER* 1.3 62.4 + - - +
150A PRO* 4.1 1.6 - - - +
152A CYS* 5.0 3.1 - - - -
182A ILE* 5.0 7.3 - - - +
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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