Contacts of the strand formed by residues 162 - 172 (chain M) in PDB entry 2GTL
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 VAL 162 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129M ILE* 6.5 0.7 - - + -
152M SER* 4.1 10.8 - - - -
153M TYR* 3.3 23.1 - - - +
154M GLU* 3.9 7.0 - - + +
155M LEU* 3.4 7.0 - - - -
160M HIS 3.9 8.5 - - - +
161M THR* 1.3 82.4 - - - +
163M SER* 1.3 71.0 + - - +
164M THR* 3.7 9.9 + - - +
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Residues in contact with SER 163 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152M SER* 3.0 26.2 - - - -
153M TYR* 3.1 38.8 + - - -
155M LEU* 2.9 21.8 - - - +
162M VAL* 1.3 68.8 - - - +
164M THR* 1.3 65.8 + - - +
165M THR* 3.8 10.2 + - - -
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Residues in contact with THR 164 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150M THR* 4.4 18.4 - - + -
151M LEU 3.5 3.1 - - - +
152M SER* 3.1 23.5 + - - +
162M VAL* 3.7 14.0 + - - +
163M SER* 1.3 78.1 + - - +
165M THR* 1.3 60.2 + - - +
166M GLN* 4.1 2.9 + - + +
186M GLN* 4.9 1.9 - - - +
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Residues in contact with THR 165 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150M THR* 3.4 4.0 - - - -
151M LEU* 3.0 43.5 + - - +
153M TYR* 4.9 2.4 + - - -
163M SER* 3.8 12.3 + - - -
164M THR* 1.3 75.6 - - - +
166M GLN* 1.3 68.9 + - - +
167M LEU* 4.0 7.2 - - - +
182M PRO* 4.5 7.6 - - + -
186M GLN* 3.7 24.9 - - + +
189M GLY* 4.2 26.9 - - - +
190M TYR 4.6 9.0 + - - +
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Residues in contact with GLN 166 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148M ARG* 5.6 2.4 - - - -
149M ALA 3.7 4.7 - - - +
150M THR* 4.6 13.9 - - + +
164M THR* 4.1 3.1 + - + +
165M THR* 1.3 73.4 - - - +
167M LEU* 1.3 67.9 + - - +
182M PRO* 3.4 1.4 - - - +
183M LEU* 3.3 30.0 + - + +
186M GLN* 3.1 37.9 + - - +
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Residues in contact with LEU 167 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130M VAL* 4.7 0.4 - - + -
148M ARG* 3.5 12.8 - - - +
149M ALA 2.7 33.7 + - - +
150M THR 4.4 2.0 - - - -
151M LEU* 3.7 23.1 - - + +
165M THR* 4.0 13.2 - - - +
166M GLN* 1.3 83.9 - - - +
168M ARG* 1.3 61.7 + - - +
180M LEU* 3.6 21.1 - - + -
181M ALA* 3.0 27.4 - - - +
182M PRO* 3.4 5.8 - - + -
183M LEU* 4.4 7.1 - - - +
190M TYR 3.4 17.3 - - - +
191M GLY* 4.5 0.7 - - - -
192M VAL* 3.6 31.2 - - + -
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Residues in contact with ARG 168 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B ARG 5.3 6.7 + - - -
125B TYR 5.4 5.3 + - - -
147M LEU 3.6 7.2 - - - +
148M ARG* 4.0 34.6 - - + +
167M LEU* 1.3 73.9 - - - +
169M GLY* 1.3 66.2 + - - +
180M LEU* 3.3 5.9 - - - -
181M ALA* 2.8 34.4 + - + +
182M PRO 5.3 3.4 - - - +
183M LEU* 3.7 40.3 + - + +
184M LYS* 4.7 5.1 - - - +
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Residues in contact with GLY 169 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B GLY 5.9 2.0 - - - -
146M TRP* 3.5 7.0 - - - +
147M LEU* 2.7 40.8 + - - +
168M ARG* 1.3 86.2 - - - +
170M PHE* 1.3 62.1 + - - +
179M LEU 3.4 11.4 - - - -
180M LEU* 4.0 1.6 - - - -
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Residues in contact with PHE 170 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B ALA 4.0 4.3 - - - -
119B ALA* 3.8 6.3 - - - -
122B GLY* 3.5 41.1 - - - -
144M ARG* 3.2 38.6 - - + -
145M VAL 3.6 11.9 - - - +
146M TRP* 3.8 31.4 - + + -
147M LEU* 3.5 9.8 - - - +
169M GLY* 1.3 76.0 - - - +
171M TYR* 1.3 70.3 + - - +
172M ASN* 4.5 10.3 - - + -
177M GLU* 5.2 2.0 - - - -
178M LEU* 3.7 5.0 - - - +
179M LEU* 3.2 52.4 + - + +
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Residues in contact with TYR 171 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99M THR 4.9 2.4 + - - -
101M SER* 4.5 10.5 + - - -
104M ILE* 3.7 28.6 - - + +
105M THR* 3.4 34.5 - - + -
143M ASN 4.3 1.6 - - - +
144M ARG* 3.9 11.4 - - - -
145M VAL* 3.6 15.0 + - + +
147M LEU* 4.4 2.0 - - + -
170M PHE* 1.3 80.4 - - - +
172M ASN* 1.3 64.5 + - - +
173M PHE* 3.6 42.4 + + - -
176M ARG* 3.6 47.5 + - - +
177M GLU 3.4 18.4 - - - -
178M LEU* 4.0 13.9 - - + -
196M PHE* 5.0 0.7 - + - -
201M ASP* 5.2 0.3 + - - -
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Residues in contact with ASN 172 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79M ASP* 3.2 35.1 + - - +
143M ASN* 5.2 0.8 + - - -
144M ARG* 4.2 23.5 + - - +
170M PHE* 4.1 14.6 - - + -
171M TYR* 1.3 73.1 - - - +
173M PHE* 1.3 56.0 + - - +
174M GLY* 2.8 19.4 - - - +
175M LYS* 3.5 19.0 - - + +
176M ARG* 2.7 35.3 + - - -
177M GLU* 2.9 22.6 + - + +
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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