Contacts of the strand formed by residues 118 - 121 (chain O) in PDB entry 1U8F
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 ARG 118 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93O GLU 3.2 3.1 + - - +
94O TYR* 3.4 29.3 - - + -
95O VAL* 2.9 24.4 + - - +
112O LEU* 4.4 0.4 - - - -
116O ALA* 4.4 1.4 - - - +
117O LYS* 1.3 87.6 - - + +
119O VAL* 1.3 68.1 + - - +
120O ILE* 4.4 0.9 - - - -
140O TYR* 3.2 22.2 + - - -
142O ASN* 2.9 38.7 + - - +
144O LEU 2.8 33.0 + - - +
145O LYS* 3.2 16.2 - - - +
331O MET* 3.6 15.9 - - + -
335O GLU* 2.7 35.8 + - - -
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Residues in contact with VAL 119 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95O VAL* 3.3 11.7 - - + +
97O GLU* 4.0 22.9 - - + -
108O ALA* 3.7 33.4 - - + +
111O HIS* 3.8 23.6 - - + -
112O LEU* 4.1 17.3 - - + -
116O ALA* 5.0 0.7 - - + -
118O ARG* 1.3 78.6 - - - +
120O ILE* 1.3 69.0 + - - +
121O ILE* 4.0 2.0 - - + -
145O LYS 2.7 13.7 + - - +
146O ILE* 3.5 8.6 - - + -
147O ILE* 3.0 30.3 + - - +
331O MET* 5.2 0.5 - - - +
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Residues in contact with ILE 120 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94O TYR* 4.0 17.3 - - + -
95O VAL 2.8 17.4 + - - +
96O VAL* 3.4 9.4 - - + +
97O GLU 2.9 24.4 + - - -
118O ARG 4.3 0.2 - - - +
119O VAL* 1.3 81.2 - - - +
121O ILE* 1.3 70.2 + - - +
122O SER 3.4 1.0 + - - -
147O ILE* 3.5 8.5 - - + +
149O ASN* 4.5 5.6 - - + +
324O VAL* 4.4 18.2 - - + -
327O LEU* 4.0 22.0 - - + -
328O MET* 4.0 21.8 - - + -
331O MET* 3.6 39.0 - - + -
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Residues in contact with ILE 121 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97O GLU* 3.7 15.5 - - + +
102O PHE 4.5 2.0 - - - +
103O THR* 3.3 46.0 - - + +
104O THR 4.5 0.9 - - - +
108O ALA* 3.7 30.5 - - + -
119O VAL* 4.6 3.4 - - + -
120O ILE* 1.3 71.6 - - - +
122O SER* 1.3 61.7 + - - +
123O ALA* 2.9 28.9 + - + +
125O SER* 4.2 2.0 - - - +
128O ALA* 4.0 23.8 - - + -
146O ILE* 4.1 5.8 - - + -
147O ILE 2.8 15.9 + - - +
148O SER* 3.5 2.5 - - - -
149O ASN* 3.0 23.6 + - - +
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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
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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