Contacts of the strand formed by residues 155 - 165 (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 GLY 155 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A ASN* 3.3 13.5 - - - -
105A ILE* 5.3 2.5 - - - -
153A ILE* 3.7 3.4 + - - -
154A VAL* 1.3 80.6 - - - +
156A LYS* 1.3 60.3 + - - -
157A PHE* 3.5 11.9 - - - -
181A TYR* 3.5 4.6 - - - -
182A ILE 2.9 28.5 + - - -
183A LEU* 5.9 0.9 - - - -
239A LEU* 4.1 13.7 - - - -
249A LEU* 6.3 0.2 - - - -
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Residues in contact with LYS 156 (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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20A ASN* 3.1 30.7 + - - +
23A GLU* 5.8 3.8 - - - +
73A LYS* 6.1 4.3 - - - +
104A VAL 4.6 0.3 - - - +
105A ILE* 3.9 5.9 - - - +
155A GLY* 1.3 68.9 - - - -
157A PHE* 1.3 61.4 + - - +
158A ARG* 5.4 3.3 - - - +
179A ASP* 4.2 33.2 + - + +
180A THR 3.4 8.5 - - - +
181A TYR* 3.0 49.1 + - + +
236A ASP* 3.5 11.5 + - - -
239A LEU* 4.1 7.0 - - + +
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Residues in contact with PHE 157 (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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103A TYR* 4.1 17.5 - - + -
104A VAL 3.2 11.0 - - - +
105A ILE* 3.4 42.0 - - + -
114A GLY 4.7 0.9 - - - -
117A ILE* 3.4 28.9 - - + -
130A TRP* 5.6 0.2 - + - -
152A CYS* 3.9 12.1 - - - -
153A ILE* 3.2 30.3 - - + -
154A VAL 4.7 0.2 - - - -
155A GLY* 3.5 21.5 - - - -
156A LYS* 1.3 78.0 - - - +
158A ARG* 1.3 67.8 + - - +
179A ASP* 3.6 5.6 - - - +
180A THR* 2.8 37.5 + - - +
182A ILE* 3.8 23.3 - - + -
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Residues in contact with ARG 158 (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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23A GLU* 3.5 41.1 - - - +
24A ASP* 2.7 37.8 + - - -
25A ASP* 4.7 1.0 - - - +
26A LEU* 4.8 3.4 - - - +
102A GLU 3.7 0.5 - - - +
103A TYR* 3.2 8.7 - - - -
104A VAL* 2.9 47.9 + - + +
105A ILE* 4.3 3.2 - - - +
106A GLY 3.1 33.5 + - - +
156A LYS 5.4 3.1 - - - +
157A PHE* 1.3 74.0 - - - +
159A MET* 1.3 59.1 + - - +
160A TYR* 4.0 32.0 + - + -
174A ARG* 3.2 30.1 - - - +
179A ASP* 3.9 7.2 - - - +
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Residues in contact with MET 159 (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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50A VAL* 4.1 22.7 - - + -
52A LEU* 4.1 14.1 - - + -
84A VAL* 4.0 25.4 - - + -
86A ILE* 6.1 0.9 - - + -
101A VAL* 3.3 31.6 - - + -
102A GLU 3.5 3.1 - - - -
103A TYR* 3.3 35.7 - - + +
146A ILE* 4.2 2.2 - - + -
157A PHE 4.2 0.8 + - - -
158A ARG* 1.3 72.1 - - - +
160A TYR* 1.3 79.5 + - - +
161A VAL* 5.5 3.4 - - + -
172A THR* 5.3 1.6 - - - +
173A SER 4.8 4.2 - - - +
174A ARG* 5.5 0.4 - - - +
175A ASN* 5.2 4.6 + - - +
178A THR* 4.1 36.1 + - - +
179A ASP* 5.0 1.6 + - - -
180A THR* 5.0 0.4 - - - +
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Residues in contact with TYR 160 (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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25A ASP* 3.5 9.6 + - - -
26A LEU* 3.5 34.4 - - + +
101A VAL* 3.3 10.7 - - - +
102A GLU* 2.8 45.9 + - - +
104A VAL* 3.8 19.5 - - + -
158A ARG* 4.0 27.8 + - + -
159A MET* 1.3 80.8 - - - +
161A VAL* 1.3 63.8 + - - +
162A ALA 4.2 0.2 - - - -
171A ARG* 3.8 15.0 - - + -
172A THR* 3.5 26.9 - - - -
173A SER 3.7 23.1 - - - -
174A ARG* 3.4 27.0 - - + +
175A ASN 5.6 0.2 - - - -
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Residues in contact with VAL 161 (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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47A VAL* 3.9 26.4 - - + +
50A VAL* 4.2 24.7 - - + -
86A ILE* 4.5 13.2 - - + -
99A PHE* 3.7 32.3 - - + -
100A ARG 3.5 7.6 - - - +
101A VAL* 4.9 8.1 - - + -
159A MET* 5.5 3.6 - - + -
160A TYR* 1.3 78.4 - - - +
162A ALA* 1.3 63.7 + - - +
163A VAL* 4.8 3.7 - - + +
170A LEU 3.7 0.7 - - - +
171A ARG* 3.3 3.8 - - - +
172A THR* 3.1 37.8 + - + +
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Residues in contact with ALA 162 (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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99A PHE* 2.9 26.9 - - - +
100A ARG* 2.8 27.0 + - + +
102A GLU* 3.9 26.0 - - + +
160A TYR 4.2 0.6 - - - -
161A VAL* 1.3 74.1 - - - +
163A VAL* 1.3 61.7 + - - +
164A TRP* 4.9 2.8 - - + -
169A VAL* 3.7 20.9 - - + -
170A LEU 3.2 5.2 - - - -
171A ARG* 4.2 4.7 - - - +
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Residues in contact with VAL 163 (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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43A GLU 3.9 8.1 - - - +
45A LEU* 3.8 46.2 - - + +
46A ASN* 5.0 4.3 - - - +
47A VAL* 4.6 17.5 - - + +
88A PHE* 5.1 0.2 - - + -
97A ASP* 5.9 0.4 - - - +
98A LEU 3.4 11.0 - - - +
99A PHE* 4.3 7.9 - - + -
161A VAL* 4.8 2.7 - - + +
162A ALA* 1.3 78.5 - - - +
164A TRP* 1.3 73.2 + - - +
169A VAL* 3.7 2.6 - - - -
170A LEU* 2.6 54.6 + - + +
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Residues in contact with TRP 164 (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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43A GLU 2.5 26.7 + - - -
98A LEU* 2.7 61.0 + - + +
99A PHE* 4.9 3.1 - - - -
100A ARG* 3.0 47.3 - - - -
162A ALA* 4.1 6.2 - - + -
163A VAL* 1.3 75.4 - - - +
165A THR* 1.3 61.8 - - - +
166A PRO* 4.8 0.5 - - - +
168A GLY 4.1 8.7 - - - -
169A VAL* 3.9 25.2 - - + +
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Residues in contact with THR 165 (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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43A GLU* 2.8 46.0 + - + +
163A VAL 3.6 0.2 + - - -
164A TRP* 1.3 77.6 - - - +
166A PRO* 1.3 71.8 - - + +
167A TYR* 3.1 34.8 - - + +
168A GLY 2.4 34.8 + - - +
170A LEU* 3.4 22.4 - - + +
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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