Contacts of the strand formed by residues 110 - 117 (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 SER 110 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108M GLY 3.3 5.1 + - - -
109M SER* 1.3 78.5 + - - +
111M TYR* 1.3 64.0 + - - +
112M THR* 4.4 1.5 + - - +
129M ILE* 3.4 18.2 - - - +
130M VAL 3.6 3.8 - - - -
131M THR* 3.0 23.5 - - - +
224M ARG* 3.4 7.4 - - - +
225M TYR* 3.0 46.4 + - - -
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Residues in contact with TYR 111 (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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104M ILE* 2.8 41.9 + - - +
109M SER* 2.9 20.8 + - - -
110M SER* 1.3 75.3 - - - +
112M THR* 1.3 61.6 + - - +
128M ALA 4.6 0.2 - - - -
129M ILE* 3.5 1.9 - - - +
130M VAL* 2.8 56.6 + - + +
132M ILE* 4.8 4.5 - - + -
178M LEU* 4.1 16.6 - - + -
194M CYS* 5.5 0.2 - - - -
196M PHE* 3.4 37.7 - + + -
201M ASP 4.1 0.2 - - - -
202M ASP 4.5 2.0 - - - -
204M ALA* 5.5 1.1 - - + -
206M CYS* 5.0 2.2 - - - -
220M PHE* 4.7 0.9 - - - -
222M ALA* 4.2 12.6 - - + -
223M GLN 3.2 6.5 - - - +
224M ARG* 3.3 42.0 + - + -
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Residues in contact with THR 112 (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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110M SER* 5.4 2.0 - - - +
111M TYR* 1.3 75.7 - - - +
113M GLY* 1.3 73.1 + - - +
127M HIS* 4.4 10.6 - - - -
128M ALA 2.9 16.5 + - - -
129M ILE* 3.9 18.3 - - + +
220M PHE* 4.6 0.2 - - - -
222M ALA* 3.5 7.2 - - - +
223M GLN* 2.8 40.4 + - - +
225M TYR* 3.9 30.9 - - + +
72N ASN* 3.6 6.0 + - - +
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Residues in contact with GLY 113 (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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112M THR* 1.3 81.9 + - - +
114M LEU* 1.3 61.8 + - - -
115M ALA 3.8 0.2 - - - -
127M HIS* 3.6 9.0 - - - -
128M ALA 3.1 25.7 + - - -
220M PHE* 3.8 10.8 - - - -
221M ASN 3.4 17.7 - - - -
72N ASN* 3.6 9.9 - - - -
73N GLU* 5.0 0.4 - - - -
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Residues in contact with LEU 114 (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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113M GLY* 1.3 70.9 - - - -
115M ALA* 1.3 62.3 + - - +
116M THR* 3.5 12.5 + - - +
125M PRO* 4.0 13.9 - - + +
126M ASP* 3.0 36.3 - - - +
127M HIS* 3.6 19.7 - - + +
220M PHE* 3.3 13.7 - - - +
221M ASN 4.3 1.3 + - - +
72N ASN 3.3 8.3 + - - -
73N GLU* 3.3 41.5 - - + +
74N GLN* 3.9 10.5 + - - +
75N GLU* 3.8 4.0 - - - +
90N HIS* 3.3 36.1 - - + +
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Residues in contact with ALA 115 (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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113M GLY 3.6 1.8 + - - -
114M LEU* 1.3 71.3 - - - +
116M THR* 1.3 59.6 + - - +
117M TRP* 3.9 11.2 - - + +
125M PRO* 3.0 4.2 - - - +
126M ASP* 2.6 53.8 + - - +
128M ALA* 3.6 22.9 - - + -
153M TYR* 5.5 0.4 - - + -
208M ILE* 4.3 9.0 - - + -
218M ALA* 5.0 1.3 - - + -
219M HIS 3.7 1.8 - - - +
220M PHE* 3.3 18.2 - - + +
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Residues in contact with THR 116 (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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114M LEU 3.5 12.3 - - - +
115M ALA* 1.3 72.3 - - - +
117M TRP* 1.3 64.6 + - - +
118M THR* 3.7 5.7 + - - +
125M PRO* 4.1 19.7 - - + -
218M ALA* 4.0 1.6 - - - -
219M HIS* 3.1 38.5 + - + +
220M PHE* 5.2 0.2 - - - -
74N GLN* 3.5 23.6 - - + +
75N GLU* 5.1 4.3 - - - -
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Residues in contact with TRP 117 (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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9G GLU* 4.4 2.1 - - - +
115M ALA* 4.0 6.4 - - - +
116M THR* 1.3 77.3 + - - +
118M THR* 1.3 59.3 - - - +
119M SER 3.8 2.0 - - - +
121M GLU* 3.9 43.5 - - + +
123M LEU* 3.8 28.4 + - + +
124M ASN 5.0 1.1 - - - -
125M PRO* 5.1 2.7 - - - +
126M ASP* 3.1 29.5 + - - -
153M TYR* 3.6 48.0 - + + -
190M TYR* 4.0 17.0 - + - -
208M ILE* 3.8 20.4 - - + -
217M CYS* 3.9 19.3 - - + +
218M ALA* 3.3 23.8 - - + -
251M CA 3.9 15.9 - - - -
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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