Contacts of the strand formed by residues 136 - 143 (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 LYS 136 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2E ALA 2.8 40.8 + - - +
3E GLU* 4.0 6.5 - - - +
4E TYR* 4.0 37.0 - - + +
41E ASN* 4.8 1.0 + - - -
44E VAL* 4.5 18.1 - - + +
130G TRP* 3.5 9.5 - - - -
131G ASP* 2.7 37.2 + - - +
134G GLY* 3.2 19.5 - - - +
135G ASN* 1.3 74.5 - - - +
137G LEU* 1.3 68.0 + - - +
138G LEU* 3.8 16.8 + - + -
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Residues in contact with LEU 137 (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* 5.0 5.2 - - + -
98G ALA* 4.7 8.5 - - + -
99G ILE* 3.9 37.0 - - + +
102G ALA* 4.0 24.3 - - + +
103G PHE* 3.9 17.3 - - + -
128G LEU* 4.1 17.7 - - + -
129G GLY 3.5 8.3 - - - +
130G TRP* 3.7 21.7 - - + -
136G LYS* 1.3 73.6 - - - +
138G LEU* 1.3 69.4 + - - +
156G LEU* 3.6 29.2 - - + -
194G TYR* 4.3 9.4 - - + -
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Residues in contact with LEU 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E TYR* 3.7 10.5 - - - +
44E VAL* 4.7 12.8 - - + -
47E LEU* 6.3 1.3 - - + -
66E LEU* 4.7 20.6 - - + -
70E LEU* 3.7 31.0 - - + -
103G PHE* 4.2 5.8 - - + -
127G ALA 3.8 0.2 - - - +
128G LEU* 3.5 2.5 - - - +
129G GLY* 2.7 39.5 + - - +
131G ASP* 3.8 17.3 - - + -
136G LYS* 4.2 15.5 - - + +
137G LEU* 1.3 82.5 - - - +
139G ILE* 1.3 66.4 + - - +
140G PHE* 4.0 21.7 - - + -
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Residues in contact with ILE 139 (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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63E GLU* 2.8 29.5 - - - +
66E LEU* 3.7 12.9 - - - +
103G PHE* 3.5 33.4 - - + -
109G PHE* 3.8 25.1 - - + +
112G GLN* 3.5 29.1 + - + +
113G PHE* 3.9 23.3 - - + +
116G ALA* 4.1 15.9 - - + -
126G ALA* 5.5 0.2 - - + -
127G ALA 3.3 8.5 - - - +
128G LEU* 4.3 6.7 - - + -
138G LEU* 1.3 76.3 - - - +
140G PHE* 1.3 69.9 + - - +
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Residues in contact with PHE 140 (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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63E GLU* 3.7 4.3 - - - -
66E LEU* 4.2 22.0 - - + -
67E ALA* 4.5 9.6 - - + -
70E LEU* 4.4 2.9 - - + -
151E LEU* 5.7 1.8 - - + -
116G ALA* 4.8 0.4 - - - +
126G ALA* 3.8 3.3 - - - +
127G ALA* 2.8 40.1 + - + +
129G GLY* 4.6 4.3 - - - -
138G LEU* 4.0 35.0 - - + -
139G ILE* 1.3 84.6 - - - +
141G GLN* 1.3 63.2 + - - +
142G VAL* 3.8 7.6 + - + -
148G ASN 4.3 11.2 - - - +
149G PHE* 4.1 17.9 - - + -
150G PRO* 3.5 23.1 - - + -
153G ILE* 3.6 44.6 - - + -
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Residues in contact with GLN 141 (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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59E ILE* 5.1 0.6 - - - +
60E LEU* 3.9 26.5 - - - +
63E GLU* 4.0 27.5 + - + +
116G ALA* 3.0 29.1 + - + +
119G THR* 2.7 41.0 + - - -
120G VAL* 3.7 15.0 - - + +
125G TRP 3.7 3.6 - - - +
126G ALA* 5.0 0.7 - - - +
140G PHE* 1.3 72.9 - - - +
142G VAL* 1.3 62.1 + - - +
143G TYR* 3.5 23.8 + - + -
148G ASN* 3.0 30.6 + - - +
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Residues in contact with VAL 142 (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* 4.6 8.7 - - + -
75G ASN* 5.1 1.8 - - - +
120G VAL* 4.5 2.3 - - - +
124G GLY* 3.0 5.4 - - - -
125G TRP* 3.0 47.6 + - + +
127G ALA* 4.4 21.5 - - + -
140G PHE* 4.7 5.8 - - + +
141G GLN* 1.3 72.8 - - - +
143G TYR* 1.3 75.5 + - - +
144G ASP 4.2 2.9 - - - +
145G HIS* 3.8 25.6 - - - +
147G THR 3.3 11.4 - - - +
148G ASN* 4.4 0.4 - - - -
149G PHE* 3.6 23.8 - - + -
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Residues in contact with TYR 143 (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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60E LEU* 4.5 13.4 + - + +
64E LYS* 3.7 29.0 - - + +
120G VAL* 4.5 13.2 - - + -
121G GLN 5.6 2.2 - - - -
123G CYS 3.8 5.6 - - - +
141G GLN* 3.5 34.0 + - - -
142G VAL* 1.3 78.3 - - - +
144G ASP* 1.3 75.3 + - - +
145G HIS 2.9 4.9 + - - -
147G THR* 2.8 47.5 + - + -
148G ASN* 3.4 27.1 + - + -
64H LYS* 4.6 15.2 + - - -
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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