Contacts of the strand formed by residues 124 - 131 (chain G) in PDB entry 1GN2
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 124 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120G VAL* 3.8 10.9 - - - +
122G GLY 4.0 0.6 + - - -
123G CYS* 1.3 76.0 - - - +
125G TRP* 1.3 63.6 + - - -
142G VAL 3.0 14.8 - - - -
144G ASP 3.6 11.9 - - - -
161G MET* 2.9 31.4 + - - -
162G TRP* 3.4 9.9 - - - +
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Residues in contact with TRP 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75G ASN* 3.4 43.8 - - + +
76G HIS* 3.8 21.5 - + - -
79G TRP* 4.0 18.2 - + + -
120G VAL* 4.5 6.6 - - - +
124G GLY* 1.3 76.3 - - - -
126G ALA* 1.3 65.1 + - - +
127G ALA* 5.4 1.3 - - + -
141G GLN* 3.7 6.9 - - - +
142G VAL* 3.0 45.1 + - + +
144G ASP 3.2 21.7 + - - -
145G HIS* 3.2 22.0 + - - -
158G LEU* 3.6 31.9 - - + -
159G LEU 3.3 10.3 - - - -
160G ASP* 3.3 47.3 - - + -
161G MET* 4.1 3.8 - - - +
162G TRP* 4.0 3.2 - - - +
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Residues in contact with ALA 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113G PHE* 3.6 26.8 - - + +
116G ALA* 4.3 6.1 - - + -
117G ALA* 3.4 37.9 - - + +
125G TRP* 1.3 74.6 - - - +
127G ALA* 1.3 61.7 + - - +
139G ILE* 5.5 0.4 - - + -
140G PHE 3.8 4.7 - - - -
141G GLN* 5.0 0.9 - - - +
158G LEU* 3.3 3.5 - - - +
159G LEU 2.9 31.1 + - - +
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Residues in contact with ALA 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151E LEU* 4.5 9.9 - - + -
113G PHE* 4.0 5.8 - - - -
125G TRP* 5.4 0.7 - - + -
126G ALA* 1.3 74.6 - - - +
128G LEU* 1.3 63.7 + - - +
129G GLY 3.9 0.2 + - - -
138G LEU 3.8 0.2 - - - +
139G ILE* 3.3 3.4 - - - +
140G PHE* 2.8 47.3 + - + +
142G VAL* 4.4 17.5 - - + -
155G PRO* 6.0 0.4 - - + -
157G LEU 3.2 4.7 - - - -
158G LEU* 3.0 27.6 - - + -
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Residues in contact with LEU 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95G LEU* 5.7 1.3 - - + -
99G ILE* 5.0 7.6 - - + -
103G PHE* 3.9 22.4 - - + -
109G PHE* 3.8 28.9 - - + -
113G PHE* 3.9 12.9 - - + -
127G ALA* 1.3 75.7 - - - +
129G GLY* 1.3 59.5 + - - +
137G LEU* 4.1 16.2 - - + -
138G LEU 3.5 14.4 - - - +
139G ILE* 4.3 2.9 - - + +
140G PHE* 5.4 0.2 - - - -
155G PRO* 3.9 2.8 - - - +
156G LEU* 2.9 50.6 + - + -
157G LEU* 2.8 25.8 + - + +
158G LEU* 4.9 0.2 - - - +
187G TRP* 5.8 0.2 - - + -
190G VAL* 4.7 9.4 - - + -
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Residues in contact with GLY 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127G ALA 3.9 1.0 + - - -
128G LEU* 1.3 76.8 - - - +
130G TRP* 1.3 63.9 + - - -
131G ASP 4.1 0.2 - - - -
137G LEU* 3.5 6.2 - - - +
138G LEU* 2.7 35.6 + - - +
140G PHE* 4.6 3.8 - - - -
153G ILE* 4.4 13.2 - - - -
154G VAL 3.0 13.7 - - - -
155G PRO* 4.3 1.6 - - - -
156G LEU* 4.2 6.3 - - - -
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Residues in contact with TRP 130 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129G GLY* 1.3 74.3 - - - -
131G ASP* 1.3 66.0 + - - +
132G THR* 3.6 28.1 + - + +
135G ASN* 3.3 51.4 - - + +
136G LYS* 3.5 20.9 - - - -
137G LEU* 3.7 15.5 - - + -
153G ILE* 3.3 5.4 - - - +
154G VAL* 2.6 39.2 + - + +
156G LEU* 4.3 10.3 - - + +
194G TYR* 4.2 13.9 - + - -
197G ALA* 3.7 39.0 + - + -
198G THR* 3.7 28.5 - - + -
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Residues in contact with ASP 131 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E TYR* 3.0 22.9 + - - -
70E LEU* 4.3 10.9 - - + +
74E VAL* 4.7 5.2 - - - +
129G GLY 4.0 0.6 + - - -
130G TRP* 1.3 72.4 - - - +
132G THR* 1.3 55.9 + - - +
133G LEU* 3.1 18.6 + - - +
134G GLY* 2.6 28.9 + - - -
135G ASN* 2.7 35.9 + - - -
136G LYS* 2.7 19.6 + - - +
138G LEU* 3.8 15.2 - - + +
153G ILE* 3.4 20.1 - - + +
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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