Contacts of the strand formed by residues 126 - 131 (chain E) in PDB entry 2GJ6
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 GLU 126 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D ASP* 5.6 1.9 - - - +
136D LYS* 5.8 1.7 + - - +
124E PRO 3.8 2.0 + - - +
125E PRO* 1.3 74.6 - - - +
127E VAL* 1.3 59.8 + - - +
148E LEU 3.3 1.6 - - - +
149E ALA* 3.2 3.8 - - - -
150E THR* 2.6 55.5 + - - +
151E GLY* 6.5 0.2 - - - -
189E ARG* 5.5 4.9 + - - -
237E VAL* 5.1 1.1 - - - -
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Residues in contact with VAL 127 (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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132D LYS* 5.4 0.7 + - - -
125E PRO* 4.4 4.5 - - + +
126E GLU* 1.3 80.5 - - - +
128E ALA* 1.3 63.8 + - - +
147E CYS* 3.9 22.7 - - - -
148E LEU 3.3 2.7 - - - -
149E ALA* 4.3 5.6 - - + -
212E CYS 4.2 5.6 - - - +
214E VAL* 3.9 19.5 - - + -
237E VAL* 3.8 41.1 - - + +
238E SER 4.1 4.8 - - - +
239E ALA* 3.5 33.3 - - + +
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Residues in contact with ALA 128 (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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130D ASP* 5.0 3.8 - - + +
131D SER* 5.9 0.4 - - - +
132D LYS* 6.0 0.2 - - - +
134D SER* 4.0 28.5 - - - +
136D LYS* 5.6 1.8 - - - +
127E VAL* 1.3 76.0 - - - +
129E VAL* 1.3 62.9 + - - +
130E PHE* 3.9 18.2 + - + -
147E CYS* 3.4 3.8 - - - -
148E LEU* 2.8 39.4 + - + +
239E ALA* 3.8 4.9 - - - -
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Residues in contact with VAL 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D ASP* 3.8 2.3 - - - +
131D SER* 3.0 31.9 + - - -
128E ALA* 1.3 72.3 - - - +
130E PHE* 1.3 75.3 + - - +
145E LEU* 4.0 14.1 - - + -
146E VAL 3.6 6.1 - - - +
147E CYS* 4.5 0.4 - - - -
161E TRP* 4.3 9.4 - - + -
210E PHE 5.1 1.1 - - - +
212E CYS* 3.7 24.7 - - + +
239E ALA* 3.4 33.7 - - + +
240E GLU* 3.9 12.8 - - - +
241E ALA* 3.8 24.0 - - + +
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Residues in contact with PHE 130 (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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128D LEU* 3.7 18.6 - - + -
129D ARG 3.6 7.0 - - - +
130D ASP* 3.6 32.3 - - + -
134D SER* 4.2 7.0 - - - -
136D LYS* 3.7 39.5 - - + -
137D SER* 3.8 11.7 - - - -
138D VAL* 4.2 9.6 - - + -
128E ALA* 3.9 17.9 - - + -
129E VAL* 1.3 89.9 - - - +
131E GLU* 1.3 61.7 + - - +
132E PRO* 4.1 0.7 - - - +
145E LEU* 4.0 4.7 - - - +
146E VAL* 2.8 49.4 + - + +
148E LEU* 3.9 27.8 - - + -
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Residues in contact with GLU 131 (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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128D LEU* 3.5 21.7 - - - +
129D ARG 3.0 17.0 + - - +
130D ASP 4.9 2.1 - - - +
131D SER* 3.3 33.6 - - - -
130E PHE* 1.3 78.7 - - - +
132E PRO* 1.4 72.4 - - + +
133E SER* 4.4 0.2 - - - -
145E LEU* 5.4 0.2 - - + -
203E TRP* 3.7 27.0 - - + -
241E ALA* 3.4 18.4 - - + +
242E TRP 4.5 4.2 + - - +
244E ARG* 4.8 12.1 - - - +
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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