Contacts of the strand formed by residues 117 - 120 (chain H) in PDB entry 5U0A
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 PHE 117 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60H VAL 3.4 2.2 - - - +
61H ARG* 3.0 4.9 - - - +
62H THR* 2.9 40.8 + - + +
65H ILE* 4.1 25.6 - - + -
91H VAL* 5.2 4.7 - - + -
94H VAL* 6.3 0.2 - - + -
100H ILE* 4.1 28.5 - - + -
113H THR* 3.6 39.3 - - + -
115H VAL* 3.8 5.8 - - + -
116H LEU* 1.3 74.7 - - - +
118H TYR* 1.3 58.8 + - - +
119H LEU* 3.9 26.0 - - + -
160H LEU* 4.6 16.6 - - + -
172H ARG* 6.3 0.7 - - - -
174H LEU* 3.7 35.4 - - + -
177H LEU* 5.1 1.8 - - + -
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Residues in contact with TYR 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H ARG* 3.0 43.9 + - - -
59H ALA* 4.1 7.9 - - + -
60H VAL 3.3 1.6 - - - -
61H ARG* 3.5 56.4 + - + +
116H LEU 3.8 3.3 + - - +
117H PHE* 1.3 76.5 - - - +
119H LEU* 1.3 61.4 + - - +
166H SER* 3.2 20.4 + - - -
167H VAL* 3.5 34.6 - - + +
170H PHE* 5.2 3.6 - - + +
171H GLY 4.1 11.2 - - - -
172H ARG* 3.1 52.8 + - + +
173H MET 6.0 1.3 - - - +
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Residues in contact with LEU 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H ALA* 4.2 2.9 - - - -
60H VAL* 2.9 35.2 + - + +
62H THR* 6.1 0.9 - - + -
65H ILE* 4.2 10.5 - - + -
117H PHE* 3.9 28.0 - - + -
118H TYR* 1.3 76.4 - - - +
120H PRO* 1.3 86.7 - - + +
123H ALA* 4.8 6.3 - - + -
124H ILE* 3.8 33.9 - - + +
127H LEU* 5.1 1.8 - - + -
160H LEU* 3.7 31.9 - - + +
162H SER* 5.2 0.9 - - - +
167H VAL* 5.3 0.2 - - - -
172H ARG* 4.4 9.4 - - - +
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Residues in contact with PRO 120 (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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57H ASP* 6.4 0.7 - - + -
58H LYS 3.7 11.2 - - - +
59H ALA* 3.8 4.0 - - + -
119H LEU* 1.3 97.8 - - + +
121H VAL* 1.3 67.4 + - - +
122H PRO* 3.5 14.6 - - + -
123H ALA* 3.3 13.2 + - + +
124H ILE 3.4 8.7 + - - -
162H SER* 3.6 30.7 - - - +
163H ARG 4.0 2.7 - - - -
164H ASN* 3.6 37.5 - - + +
167H VAL* 5.1 0.4 - - + -
172H ARG* 4.5 1.6 - - - +
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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
------------------------------------------------------------
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