Contacts of the strand formed by residues 108 - 112 (chain A) in PDB entry 3C5E
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 108 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A GLY 4.2 3.1 + - - +
107A ASP* 1.3 75.7 - - - +
109A VAL* 1.3 61.5 + - - +
110A ALA 4.1 0.7 - - - -
132A ILE* 3.5 28.4 - - + +
134A MET* 3.8 16.8 - - + -
151A MET 4.8 2.2 + - - -
152A SER* 2.9 31.9 + - - +
153A LYS* 4.4 15.8 - - - +
154A ALA* 3.8 7.0 - - - -
155A LYS* 2.9 33.1 + - + +
156A ALA 3.4 5.2 + - - -
218A ILE* 3.8 24.3 - - - +
232A GLU* 5.6 2.4 + - - -
427A VAL* 3.8 26.9 - - - +
428A ASP* 5.2 4.9 + - - -
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Residues in contact with VAL 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LEU* 4.9 4.7 - - + -
103A LEU* 3.9 26.2 - - + -
107A ASP 4.0 3.6 - - - +
108A ARG* 1.3 78.1 - - - +
110A ALA* 1.3 62.4 + - - +
111A VAL* 3.7 7.9 + - + +
126A CYS* 4.2 14.8 - - - -
131A LEU* 4.0 26.2 - - + -
132A ILE 2.8 12.1 + - - +
133A PHE* 3.5 2.3 - - - -
134A MET* 2.9 27.3 + - - +
156A ALA* 3.7 13.0 - - + -
158A VAL* 3.7 29.6 - - + -
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Residues in contact with ALA 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A VAL* 1.3 74.0 - - - +
111A VAL* 1.3 61.9 + - - +
112A VAL* 4.2 6.1 - - + -
134A MET* 3.4 20.3 - - + +
149A LEU* 3.7 27.1 - - + -
154A ALA* 4.1 4.7 - - + -
156A ALA 2.8 15.8 + - - +
157A ILE* 3.3 11.2 - - + -
158A VAL 2.8 25.7 + - - -
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Residues in contact with VAL 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A VAL* 3.9 16.6 - - + +
110A ALA* 1.3 78.8 - - - +
112A VAL* 1.3 62.5 + - - +
113A LEU* 3.9 17.8 + - + -
119A TRP* 3.6 31.6 + - + +
122A VAL* 4.0 24.5 - - + -
123A ILE* 4.1 17.7 - - + -
126A CYS* 5.1 0.2 - - - -
133A PHE* 4.6 6.1 - - + -
134A MET 3.0 7.4 + - - +
135A PRO* 3.3 10.5 - - + +
136A GLY 2.9 28.2 + - - +
158A VAL* 3.6 6.3 - - + +
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Residues in contact with VAL 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ALA* 4.9 4.7 - - + -
111A VAL* 1.3 81.7 - - - +
113A LEU* 1.4 59.6 + - - +
134A MET 5.4 0.4 - - - +
136A GLY 3.7 6.3 - - - +
137A THR 3.7 29.8 - - - +
138A ILE* 3.9 13.3 - - + +
140A MET* 3.7 23.1 - - + -
145A ILE* 5.2 7.0 - - + -
157A ILE* 4.3 20.6 - - + -
158A VAL 2.8 12.0 + - - +
159A ALA* 3.4 21.0 - - - +
160A GLY 3.8 3.3 + - - -
163A VAL* 4.2 19.2 - - + +
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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