Contacts of the strand formed by residues 116 - 119 (chain H) in PDB entry 3P1M
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 HIS 116 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74H ARG* 5.8 0.3 + - - -
103H PHE* 3.7 5.5 - - - -
113H SER 3.4 17.5 + - - +
114H THR 3.2 4.0 - - - +
115H CYS* 1.3 78.6 - - - +
117H LEU* 1.3 84.8 + - - +
118H ILE* 4.3 3.1 - - + +
138H LEU* 4.5 2.2 - - + -
141H ALA* 3.6 22.0 - - + +
142H TYR 3.6 22.7 + - - -
143H GLY 3.7 17.0 - - - -
144H LEU* 4.1 1.1 - - - -
148H SER* 2.8 31.7 + - - -
149H ARG 3.7 8.1 - - - -
150H LEU* 4.0 6.0 - - + +
167H VAL* 4.7 0.5 - - - +
168H PRO* 3.3 39.7 - - + +
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Residues in contact with LEU 117 (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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71H PHE* 4.5 6.1 - - + -
89H LEU* 4.0 26.0 - - + -
103H PHE* 3.9 20.2 - - + -
115H CYS 3.7 4.3 - - - +
116H HIS* 1.3 81.3 - - - +
118H ILE* 1.3 64.0 + - - +
119H PHE* 3.7 17.5 - - + -
148H SER* 3.4 4.3 - - - -
149H ARG 2.9 31.8 + - - +
151H GLY* 3.7 22.4 - - - -
165H VAL* 4.1 21.5 - - + -
166H ARG 3.7 16.8 - - - +
167H VAL* 4.0 17.9 - - + -
168H PRO* 4.3 0.9 - - - -
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Residues in contact with ILE 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B LYS 3.6 28.5 - - - +
183B THR* 4.0 3.7 - - + +
116H HIS* 4.3 4.5 - - - +
117H LEU* 1.3 77.2 - - - +
119H PHE* 1.3 66.1 + - - +
143H GLY 5.4 0.2 - - - +
145H THR* 3.9 29.6 - - + +
147H ARG* 3.6 18.8 - - + -
148H SER* 4.1 4.9 - - - +
165H VAL* 3.3 7.6 - - - +
166H ARG* 2.9 70.7 + - + +
168H PRO* 4.0 18.4 - - + -
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Residues in contact with PHE 119 (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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181B GLY 5.8 0.3 - - - -
182B LYS 5.8 0.2 - - - -
183B THR* 4.0 8.5 - - - +
89H LEU* 3.7 32.8 - - + -
117H LEU* 3.7 35.4 - - + -
118H ILE* 1.3 80.5 - - - +
120H GLU* 1.3 70.2 + - - +
121H ASP* 3.7 0.9 + - - +
123H ILE* 3.9 20.0 - - + -
124H TYR* 4.2 12.6 - - + +
127H LEU* 4.3 6.1 - - + -
147H ARG* 3.1 35.6 + - - +
149H ARG* 3.9 23.6 - - + -
151H GLY* 4.8 0.9 - - - -
154H ILE* 3.9 22.4 - - + -
163H MET* 4.5 4.5 - - + -
164H THR 4.6 2.2 - - - -
165H VAL* 3.7 15.5 - - + -
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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