Contacts of the strand formed by residues 108 - 115 (chain G) in PDB entry 5UWC
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 GLU 108 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104G TRP* 3.5 29.0 - - + -
106G GLY 4.0 6.0 - - - +
107G ALA* 1.3 78.3 - - - +
109G ASN* 1.3 78.3 + - - +
110G LEU* 3.4 3.5 + - - -
124G TRP* 3.4 2.7 - - - -
125G ALA* 2.6 46.6 + - + +
126G VAL 5.1 1.3 - - - +
127G GLY* 4.4 1.9 - - - -
128G PRO* 3.3 32.2 - - - +
196G THR* 4.9 4.3 - - - -
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Residues in contact with ASN 109 (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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108G GLU* 1.3 83.3 + - - +
110G LEU* 1.3 65.2 + - - +
111G THR* 3.3 15.9 + - + +
123G SER* 3.5 6.9 + - - +
124G TRP* 3.7 3.6 - - - -
125G ALA* 4.2 18.2 - - + +
196G THR* 5.2 2.6 - - - +
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Residues in contact with LEU 110 (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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107G ALA* 6.3 0.2 - - + -
108G GLU 3.4 1.6 - - - -
109G ASN* 1.3 74.2 - - - +
111G THR* 1.3 61.4 + - - +
112G CYS* 4.1 18.2 - - - -
122G CYS* 4.4 6.5 - - + -
123G SER 3.4 16.2 - - - +
124G TRP* 4.2 13.0 - - + -
138G LEU* 4.4 2.2 - - + -
182G ILE* 3.9 27.1 - - + +
184G VAL* 3.8 32.3 - - + -
196G THR* 4.3 14.7 - - + +
197G ASP* 4.0 12.1 - - - +
198G LYS* 2.9 40.0 + - + +
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Residues in contact with THR 111 (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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109G ASN* 3.6 14.4 - - + +
110G LEU* 1.3 79.4 - - - +
112G CYS* 1.3 63.2 + - - +
113G TRP* 3.5 11.0 - - - -
122G CYS* 3.3 2.4 - - - -
123G SER* 2.8 47.7 + - - -
198G LYS* 3.7 11.4 - - - +
406G IMD 5.4 2.1 - - - -
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Residues in contact with CYS 112 (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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110G LEU* 4.1 15.3 - - - -
111G THR* 1.3 79.3 - - - +
113G TRP* 1.3 66.6 + - - +
120G LEU* 4.3 2.2 - - + -
121G SER 3.3 5.8 - - - +
122G CYS* 2.9 33.0 - - - -
182G ILE* 3.5 23.8 - - + -
198G LYS* 4.5 9.1 + - - +
200G VAL* 4.4 10.2 - - + +
205G ILE* 3.5 33.0 - - + +
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Residues in contact with TRP 113 (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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111G THR* 3.5 18.2 - - - -
112G CYS* 1.3 81.8 - - - +
114G ILE* 1.3 62.3 + - - +
115G HIS* 3.4 21.9 - + - -
119G PHE 3.9 0.2 - - - +
120G LEU* 3.6 3.0 - - - +
121G SER* 2.9 51.9 + - - +
122G CYS 4.2 4.5 - - - -
123G SER* 3.4 39.3 - - - -
155G LYS* 6.1 1.8 - - - -
205G ILE* 3.3 15.3 - - - +
207G ILE* 3.8 28.3 - - + -
406G IMD 3.9 33.3 - + + -
407G EDT 2.4 45.4 + - - -
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Residues in contact with ILE 114 (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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113G TRP* 1.3 72.4 - - - +
115G HIS* 1.3 67.9 + - - +
117G VAL* 3.9 21.3 - - - +
119G PHE 3.2 12.3 - - - +
120G LEU* 3.8 21.3 - - + -
170G ILE* 4.6 3.6 - - + -
202G PHE* 3.6 44.9 - - + +
205G ILE* 3.0 9.2 + - + +
206G GLU* 3.9 22.9 - - + +
207G ILE* 2.8 29.0 + - - +
232G PHE* 3.6 29.4 - - + -
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Residues in contact with HIS 115 (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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113G TRP* 3.4 19.1 - + + -
114G ILE* 1.3 76.4 - - - +
116G ASP* 1.3 91.3 + - - +
117G VAL 3.1 4.0 + - - +
119G PHE* 2.9 49.5 + + + +
121G SER* 2.6 26.4 + - - -
166G ARG* 5.4 0.4 - - - -
206G GLU* 5.5 0.2 - - - -
207G ILE* 3.9 19.3 - - + +
407G EDT 3.3 57.6 + - - +
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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