Contacts of the strand formed by residues 126 - 132 (chain H) in PDB entry 2J28
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 126 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125H THR* 1.3 73.5 - - - +
127H GLU* 1.3 70.4 + - - -
145H ASN* 2.9 13.5 - - - -
146H VAL* 2.5 45.9 + - - +
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Residues in contact with GLU 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77H THR* 5.5 0.9 - - + -
126H GLY* 1.3 74.9 - - - -
128H HIS* 1.3 82.1 + - - +
129H GLU* 5.5 1.3 - - + +
143H ILE* 3.5 23.6 - - + -
144H VAL 2.8 8.7 - - - -
145H ASN* 4.1 8.6 + - - +
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Residues in contact with HIS 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119H ASN* 5.4 1.2 + - - -
121H VAL* 3.4 47.1 - - + +
122H LEU* 4.2 2.2 - - + -
124H THR* 3.3 50.3 + - + +
126H GLY 5.0 0.4 - - - +
127H GLU* 1.3 86.4 + - - +
129H GLU* 1.3 61.5 + - - +
130H VAL* 3.0 10.5 + - + +
143H ILE* 3.5 0.8 - - - +
144H VAL* 2.6 43.8 + - + +
146H VAL* 4.1 8.9 - - - +
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Residues in contact with GLU 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118H PRO* 5.9 2.9 - - - +
127H GLU* 5.5 1.7 - - + +
128H HIS* 1.3 70.2 - - - +
130H VAL* 1.3 62.4 + - - +
131H SER 3.9 2.7 + - - -
141H LYS* 5.3 15.3 - - + +
142H VAL 3.6 2.0 - - - -
143H ILE* 3.6 30.7 - - + +
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Residues in contact with VAL 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99H ILE* 4.7 14.6 - - + -
115H VAL* 3.8 27.8 - - + -
117H LEU* 3.7 31.4 - - + +
118H PRO* 6.5 0.7 - - - -
121H VAL* 4.4 11.9 - - + -
128H HIS* 3.0 15.7 + - + +
129H GLU* 1.3 72.6 - - - +
131H SER* 1.3 62.5 + - - +
132H PHE* 3.8 4.3 + - + +
142H VAL* 2.6 36.9 + - - +
144H VAL* 3.5 17.4 - - + +
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Residues in contact with SER 131 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115H VAL* 3.7 5.5 - - - +
116H ARG* 3.0 49.4 + - - +
117H LEU 5.4 0.4 - - - +
129H GLU 3.9 3.6 + - - -
130H VAL* 1.3 73.9 - - - +
132H PHE* 1.3 59.9 + - - +
133H GLN* 6.0 0.2 - - - +
139H PHE* 4.7 4.3 - - - +
140H ALA 2.8 22.7 + - - -
141H LYS* 3.0 39.6 - - - +
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Residues in contact with PHE 132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72H ILE* 5.6 12.1 - - + -
110H VAL* 3.3 26.9 - - + -
111H ALA* 2.9 31.0 - - + -
113H SER* 4.1 9.4 - - - -
115H VAL* 3.2 40.8 - - + +
130H VAL* 3.8 5.0 + - + +
131H SER* 1.3 75.5 - - - +
133H GLN* 1.3 91.4 + - - +
134H VAL* 3.6 21.1 - - + -
139H PHE* 3.1 1.4 - - - -
140H ALA* 2.7 41.9 + - + +
142H VAL* 6.3 1.3 - - + -
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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