Contacts of the strand formed by residues 120 - 126 (chain E) in PDB entry 6GL7
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 THR 120 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280D GLN* 5.9 0.9 + - - -
74E GLY* 3.7 18.4 - - - -
75E THR* 4.2 5.5 + - - -
118E LEU* 3.8 3.5 - - - +
119E LEU* 1.3 86.7 + - - +
121E VAL* 1.3 77.4 + - - +
122E TYR* 5.8 0.2 - - - -
146E TYR* 3.7 33.0 - - + +
147E PHE 3.2 15.0 - - - +
148E SER* 4.0 9.2 - - - +
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Residues in contact with VAL 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E LEU* 4.7 9.6 - - + -
72E LEU* 5.0 16.4 - - + -
73E TYR 3.0 11.0 - - - +
80E LEU* 3.8 14.6 - - + -
86E ILE* 5.5 1.3 - - + -
101E LEU* 6.3 1.6 - - + -
109E LEU* 4.7 10.3 - - + -
118E LEU* 3.5 31.9 - - + -
120E THR* 1.3 79.0 - - - +
122E TYR* 1.3 58.6 + - - +
146E TYR* 3.2 3.1 - - - -
147E PHE* 2.5 60.8 + - + +
149E PHE* 6.0 5.8 - - + -
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Residues in contact with TYR 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E LEU* 3.6 6.7 - - - -
73E TYR* 2.7 73.6 + + + +
74E GLY 4.0 7.0 - - - -
77E ARG* 3.2 45.4 - - + +
121E VAL* 1.3 76.3 - - - +
123E LEU* 1.3 70.0 + - - +
124E LYS* 4.4 13.1 - - + -
144E ARG* 3.6 37.8 + - + -
145E VAL 2.9 18.6 - - - +
146E TYR* 3.4 35.2 - + + -
147E PHE* 5.3 0.9 - - - -
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Residues in contact with LEU 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E LEU* 3.8 22.9 - - + -
69E GLY 5.0 1.3 - - - +
71E HIS 4.4 9.0 - - - +
72E LEU* 3.9 11.9 - - + -
73E TYR* 5.2 0.2 - - - -
83E ASN* 3.4 24.5 - - - +
86E ILE* 3.8 22.4 - - + -
95E LEU* 4.2 9.4 - - + -
122E TYR* 1.3 84.2 - - - +
124E LYS* 1.3 60.9 + - - +
125E VAL* 4.4 4.9 - - + -
143E ALA 3.6 0.9 - - - +
144E ARG* 3.5 1.6 - - - -
145E VAL* 2.9 42.2 + - + +
147E PHE* 3.5 34.1 - - + -
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Residues in contact with LYS 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E LEU* 3.1 6.2 - - - +
69E GLY* 2.8 38.8 + - - +
71E HIS 5.1 1.2 + - - -
73E TYR* 4.0 33.9 + - + -
122E TYR* 4.4 20.2 - - + -
123E LEU* 1.3 75.8 - - - +
125E VAL* 1.3 60.9 + - - +
126E PHE* 3.5 27.4 - - + -
135E GLY 4.6 10.0 + - - +
136E GLU* 5.6 4.0 + - - +
137E CYS* 3.7 29.7 - - + +
143E ALA 3.6 4.5 - - - -
144E ARG* 4.7 4.7 - - + +
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Residues in contact with VAL 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E PHE* 3.4 23.6 - - + -
53E VAL* 4.1 8.3 - - + -
66E PHE* 4.4 2.0 - - + -
67E ARG 3.2 11.9 - - - +
68E LEU* 5.0 0.9 - - - -
88E ILE* 3.5 27.8 - - + -
95E LEU* 4.6 4.7 - - + -
123E LEU* 4.2 13.0 - - + +
124E LYS* 1.3 78.5 - - - +
126E PHE* 1.3 66.5 + - - +
142E CYS* 3.0 5.9 - - - -
143E ALA 2.9 35.1 + - - +
145E VAL* 3.6 28.7 - - + -
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Residues in contact with PHE 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E PHE* 3.7 5.2 - - - -
66E PHE* 3.3 11.4 - - - -
67E ARG* 2.9 83.3 + - + +
68E LEU 4.7 0.9 - - - -
69E GLY* 4.6 4.3 - - - -
124E LYS* 3.5 31.9 - - + -
125E VAL* 1.3 74.6 - - - +
127E LEU* 1.3 60.3 + - - +
128E SER 3.5 4.0 - - - +
130E THR* 4.8 4.3 - - - -
134E GLU* 4.7 4.3 - - - -
135E GLY* 3.6 28.5 - - - -
136E GLU 4.0 4.5 - - - -
137E CYS* 3.9 7.4 - - + -
141E GLY 3.6 17.5 - - - -
142E CYS* 3.4 21.5 - - + -
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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