Contacts of the strand formed by residues 117 - 120 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60I VAL 3.4 2.0 - - - +
61I ARG* 3.0 4.7 - - - +
62I THR* 2.9 40.6 + - + +
65I ILE* 4.1 23.8 - - + -
91I VAL* 5.2 4.5 - - + -
94I VAL* 6.3 0.2 - - + -
100I ILE* 4.1 29.4 - - + -
113I THR* 3.6 38.8 - - + -
115I VAL* 3.8 4.9 - - + -
116I LEU* 1.3 74.8 - - - +
118I TYR* 1.3 58.3 + - - +
119I LEU* 3.9 26.7 - - + -
160I LEU* 4.6 17.5 - - + -
172I ARG* 6.3 0.9 - - - -
174I LEU* 3.7 34.8 - - + -
177I LEU* 5.1 1.3 - - + -
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Residues in contact with TYR 118 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I ARG* 3.0 43.9 + - - -
59I ALA* 4.1 8.3 - - + -
60I VAL 3.3 1.6 - - - -
61I ARG* 3.5 58.1 + - + +
116I LEU 3.8 2.9 + - - +
117I PHE* 1.3 76.1 - - - +
119I LEU* 1.3 60.3 + - - +
166I SER* 3.2 20.5 + - - -
167I VAL* 3.5 34.8 - - + +
170I PHE* 5.2 3.0 - - + +
171I GLY 4.1 11.2 - - - -
172I ARG* 3.1 52.6 + - + +
173I MET 6.0 1.6 - - - +
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Residues in contact with LEU 119 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59I ALA* 4.2 3.1 - - - -
60I VAL* 2.9 34.4 + - + +
62I THR* 6.1 2.7 - - + -
65I ILE* 4.2 10.1 - - + -
117I PHE* 3.9 28.0 - - + -
118I TYR* 1.3 76.1 - - - +
120I PRO* 1.3 87.0 - - + +
123I ALA* 4.8 5.8 - - + -
124I ILE* 3.8 33.7 - - + +
127I LEU* 5.1 1.1 - - + -
160I LEU* 3.7 32.5 - - + +
162I SER* 5.2 0.9 - - - +
167I VAL* 5.3 0.2 - - - -
172I ARG* 4.5 8.7 - - - +
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Residues in contact with PRO 120 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57I ASP* 6.4 0.7 - - + -
58I LYS 3.7 11.2 - - - +
59I ALA* 3.8 3.6 - - + -
60I VAL* 5.5 0.2 - - - -
119I LEU* 1.3 97.7 - - + +
121I VAL* 1.3 64.7 + - - +
122I PRO* 4.1 14.1 - - + -
123I ALA* 3.3 13.7 + - + +
124I ILE 3.4 8.1 + - - -
162I SER* 3.6 31.0 - - - +
163I ARG 4.0 2.5 - - - -
164I ASN* 3.6 37.0 - - + +
167I VAL* 5.1 0.7 - - + -
172I ARG* 4.5 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