Contacts of the strand formed by residues 116 - 119 (chain G) in PDB entry 2HEY
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 ILE 116 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75G LEU* 3.8 26.7 - - + -
106G LEU* 4.6 0.9 - - + -
110G PHE* 3.3 26.9 - - + -
114G VAL* 3.9 17.2 + - + -
115G LYS* 1.3 79.5 - - - +
117G ASP* 1.3 73.8 + - - +
128G SER* 4.0 1.2 + - - -
129G ILE* 3.0 49.5 + - + +
131G MET* 4.7 5.6 - - + -
138G ILE* 3.3 31.6 - - + -
154G LEU* 4.2 4.7 - - + -
155G THR 3.4 12.3 - - - +
156G VAL* 4.2 5.6 - - + -
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Residues in contact with ASP 117 (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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115G LYS* 4.9 1.4 - - - +
116G ILE* 1.3 80.2 - - - +
118G LEU* 1.3 59.0 + - - +
119G HIS* 3.7 3.5 + - + -
126G PRO* 3.8 17.8 - - + +
127G ILE 3.3 3.3 - - - +
128G SER* 3.5 26.3 + - - -
129G ILE* 4.8 0.4 - - - -
154G LEU* 3.3 6.5 - - - +
155G THR* 3.0 46.0 + - - +
157G ASN* 4.0 23.0 + - - +
119T TYR* 3.9 23.1 + - - -
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Residues in contact with LEU 118 (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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104G ILE* 4.1 12.8 - - + -
117G ASP* 1.3 71.7 - - - +
119G HIS* 1.3 65.3 + - - +
120G PHE* 3.7 24.5 - - + -
124G HIS* 3.9 5.2 - - - -
126G PRO* 3.4 3.3 - - - +
127G ILE* 2.8 48.2 + - + +
129G ILE* 4.2 8.2 - - + +
140G PHE* 4.0 14.6 - - + -
142G VAL* 3.9 23.6 - - + -
152G VAL* 3.7 28.9 - - + -
153G TYR 3.7 3.1 - - - +
154G LEU* 3.7 24.7 - - + -
173G LEU* 5.7 0.4 - - + -
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Residues in contact with HIS 119 (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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117G ASP* 3.7 6.4 + - + -
118G LEU* 1.3 75.0 - - - +
120G PHE* 1.3 66.7 + - - +
121G ARG 3.9 4.3 - - - +
122G GLU 5.8 0.9 - - - -
124G HIS* 3.7 14.1 - - - +
126G PRO* 3.3 35.6 - - + +
151G LYS 4.0 0.2 - - - -
152G VAL* 3.3 6.8 - - - +
153G TYR* 2.8 79.2 + + + +
155G THR* 3.0 40.9 - - + +
119T TYR* 3.7 10.9 + + - -
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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