Contacts of the strand formed by residues 155 - 165 (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 GLY 155 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B ASN* 3.2 14.1 - - - -
105B ILE* 5.5 1.6 - - - -
153B ILE* 4.0 2.5 + - - -
154B VAL* 1.3 76.1 - - - +
156B LYS* 1.3 61.0 + - - -
157B PHE* 3.9 10.2 + - - -
180B THR 3.8 0.7 - - - +
181B TYR* 3.3 5.7 - - - +
182B ILE 3.1 30.2 + - - +
183B LEU* 6.1 1.1 - - - -
239B LEU* 4.1 16.2 - - - -
249B LEU* 6.1 0.4 - - - -
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Residues in contact with LYS 156 (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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20B ASN* 3.2 31.5 + - - +
73B LYS* 4.4 9.3 - - - +
104B VAL 4.9 0.2 - - - +
105B ILE* 3.7 5.9 - - - +
155B GLY* 1.3 71.9 - - - -
157B PHE* 1.3 60.0 + - - +
158B ARG* 5.5 2.8 - - - +
179B ASP* 3.6 39.7 + - + -
180B THR 3.6 5.4 - - - +
181B TYR* 3.5 46.2 + - + +
236B ASP* 4.9 2.9 + - - +
239B LEU* 4.1 8.4 - - + +
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Residues in contact with PHE 157 (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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103B TYR* 4.1 24.0 - - + -
104B VAL 4.0 15.0 - - - -
105B ILE* 3.2 49.4 - - + -
114B GLY 4.6 1.1 - - - -
115B THR 4.9 0.4 - - - -
117B ILE* 4.0 18.6 - - + -
152B CYS* 4.2 11.4 - - - -
153B ILE* 3.6 30.5 - - + -
155B GLY* 4.0 17.0 - - - -
156B LYS* 1.3 73.1 - - - +
158B ARG* 1.3 61.9 + - - +
179B ASP* 3.3 10.1 - - - +
180B THR* 2.7 37.5 + - - +
182B ILE* 3.9 24.5 - - + -
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Residues in contact with ARG 158 (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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23B GLU* 3.6 27.9 - - - +
24B ASP* 2.4 50.3 + - - -
25B ASP* 4.2 0.8 - - - +
26B LEU* 4.3 1.2 - - - +
102B GLU 3.5 0.9 - - - +
103B TYR* 3.1 8.5 - - - -
104B VAL* 2.9 63.0 + - - +
105B ILE* 5.5 0.9 - - - +
106B GLY 3.2 20.0 + - - +
156B LYS 5.5 2.9 - - - +
157B PHE* 1.3 75.3 - - - +
159B MET* 1.3 59.0 + - - +
160B TYR* 3.0 34.4 + - + -
174B ARG* 3.7 29.2 - - - +
179B ASP* 3.8 7.0 - - - +
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Residues in contact with MET 159 (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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50B VAL* 4.0 17.5 - - + -
52B LEU* 3.9 30.1 - - + -
84B VAL* 4.5 7.2 - - + -
86B ILE* 5.8 1.3 - - + -
101B VAL* 3.4 29.2 - - + -
102B GLU 3.2 4.7 - - - -
103B TYR* 3.3 36.6 - - + +
146B ILE* 4.3 9.6 - - + -
157B PHE 4.2 1.2 + - - -
158B ARG* 1.3 73.0 - - - +
160B TYR* 1.3 74.0 + - - +
161B VAL* 5.0 7.0 - - + -
172B THR* 5.5 0.7 - - - -
173B SER 5.0 3.8 - - - +
175B ASN* 5.3 3.5 + - - +
178B THR* 4.1 35.1 + - - +
179B ASP* 5.2 0.6 + - - -
180B THR* 5.1 0.4 - - - +
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Residues in contact with TYR 160 (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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25B ASP* 2.9 22.5 + - - -
26B LEU* 3.7 33.5 + - + -
101B VAL* 3.6 2.4 - - - +
102B GLU* 2.7 48.6 + - + +
104B VAL* 3.9 14.8 - - + -
158B ARG* 3.0 45.6 + - + -
159B MET* 1.3 80.1 - - - +
161B VAL* 1.3 63.5 + - - +
162B ALA 3.9 0.2 - - - -
171B ARG* 3.8 13.2 - - - -
172B THR* 3.5 24.0 - - - +
173B SER 4.0 5.6 - - - -
174B ARG* 3.7 30.5 - - - -
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Residues in contact with VAL 161 (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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47B VAL* 4.2 15.4 - - + +
50B VAL* 3.9 28.7 - - + -
86B ILE* 3.8 33.4 - - + -
88B PHE* 5.5 2.2 - - + -
99B PHE* 4.4 13.0 - - + -
100B ARG 3.7 11.2 - - - +
101B VAL* 4.5 3.6 - - + +
159B MET* 5.0 11.2 - - + -
160B TYR* 1.3 77.0 - - - +
162B ALA* 1.3 65.1 + - - +
163B VAL* 5.0 4.3 - - + +
170B LEU 4.2 0.7 - - - +
171B ARG* 3.4 3.0 - - - -
172B THR* 2.7 40.9 + - - +
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Residues in contact with ALA 162 (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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99B PHE* 2.9 9.1 - - - +
100B ARG* 2.8 44.4 + - + +
102B GLU* 4.0 26.0 - - + +
160B TYR 3.9 1.0 + - - -
161B VAL* 1.3 74.2 - - - +
163B VAL* 1.3 61.4 + - - +
164B TRP* 5.2 2.5 - - + +
169B VAL* 3.6 20.9 - - + -
170B LEU 3.8 4.3 - - - -
171B ARG* 4.0 6.1 - - + +
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Residues in contact with VAL 163 (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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44B PHE 3.4 26.2 - - - +
45B LEU* 3.7 32.8 - - + +
46B ASN* 5.0 4.0 - - - -
47B VAL* 5.5 4.5 - - + +
88B PHE* 5.1 5.4 - - + -
98B LEU 3.5 17.3 - - - +
99B PHE* 4.0 9.4 - - + -
161B VAL* 5.0 4.9 - - + +
162B ALA* 1.3 80.2 - - - +
164B TRP* 1.3 58.5 + - - +
165B THR* 3.2 15.5 + - + +
169B VAL* 3.1 4.7 - - - +
170B LEU* 3.1 38.3 + - + +
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Residues in contact with TRP 164 (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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98B LEU* 3.0 49.9 + - + +
99B PHE* 5.0 3.4 - - - -
100B ARG* 3.9 51.3 - - + +
162B ALA* 5.2 1.7 - - + +
163B VAL* 1.3 72.4 - - - +
165B THR* 1.3 67.2 + - - +
166B PRO* 3.5 4.2 - - - +
168B GLY 6.1 0.4 - - - -
169B VAL* 4.4 24.0 - - + +
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Residues in contact with THR 165 (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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43B GLU* 3.1 45.4 - - + +
44B PHE* 3.9 9.0 - - - +
45B LEU 5.8 0.4 - - - +
163B VAL* 3.2 15.0 + - + +
164B TRP* 1.3 75.1 - - - +
166B PRO* 1.3 58.7 - - - +
167B TYR* 2.7 20.8 + - - +
168B GLY* 2.7 37.9 + - - +
170B LEU* 3.5 19.6 - - + +
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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