Contacts of the strand formed by residues 101 - 106 (chain A) in PDB entry 5VFC
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 LEU 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A TRP* 3.4 9.2 - - - -
96A SER* 2.9 38.8 + - - +
98A ASP* 4.9 1.8 - - - +
100A ASN* 1.3 89.1 - - + +
102A LEU* 1.3 62.3 + - - +
113A ILE* 4.2 5.8 - - + -
114A TRP 3.2 8.7 - - - +
115A ASP* 4.3 5.2 - - - +
116A VAL* 3.8 4.9 - - - -
122A LEU* 3.6 30.3 - - + -
137A PHE* 3.9 17.7 - - + -
141A SER 5.5 1.3 - - - +
158A VAL* 4.1 17.7 - - + -
407A EDO 3.9 22.0 - - - +
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Residues in contact with LEU 102 (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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61A ALA* 3.9 9.4 - - + -
69A ILE* 3.9 18.8 - - + -
71A ILE* 3.7 27.1 - - + -
83A ILE* 4.0 11.2 - - + -
93A VAL* 4.0 10.8 - - + -
94A ALA 3.2 15.7 - - - +
95A TRP* 3.5 37.7 - - + -
101A LEU* 1.3 73.2 - - - +
103A VAL* 1.3 59.3 + - - +
113A ILE* 3.3 6.2 - - - +
114A TRP* 2.8 43.3 + - + -
116A VAL* 3.6 19.5 - - + +
137A PHE* 3.9 4.3 - - - -
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Residues in contact with VAL 103 (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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93A VAL* 3.2 7.1 - - - +
94A ALA* 2.8 45.9 + - + +
102A LEU* 1.3 75.5 - - - +
104A SER* 1.3 61.8 + - - +
111A LEU* 4.0 29.2 - - + -
112A LYS 3.2 13.0 - - - +
113A ILE* 4.4 1.8 - - + -
114A TRP* 4.6 0.2 - - - -
125A LEU* 4.8 0.2 - - + -
135A CYS* 3.7 13.3 - - + -
136A ASN 4.6 2.2 - - - +
137A PHE* 3.6 27.1 - - + -
144A ILE* 3.8 28.9 - - + -
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Residues in contact with SER 104 (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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69A ILE* 3.7 22.7 - - - -
86A HIS* 2.6 29.1 + - - -
90A ILE* 3.9 8.1 - - - -
92A ASP 3.3 10.8 - - - -
93A VAL* 4.5 1.3 - - - -
103A VAL* 1.3 75.0 - - - +
105A ALA* 1.3 60.9 + - - +
111A LEU* 3.0 29.8 - - - +
112A LYS 2.9 7.6 + - - -
114A TRP* 2.8 17.2 + - - -
135A CYS* 4.0 3.6 - - - -
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Residues in contact with ALA 105 (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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90A ILE* 3.3 5.3 - - - +
91A SER 2.8 26.2 + - - -
92A ASP* 3.0 10.3 + - + +
104A SER* 1.3 72.7 - - - +
106A SER* 1.3 59.8 + - - +
110A THR 4.1 3.4 - - - -
111A LEU* 4.2 2.5 - - + -
132A VAL* 3.5 34.6 - - + +
133A PHE 4.1 3.1 - - - -
134A CYS 4.0 10.8 - - - +
135A CYS* 3.8 17.9 - - - -
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Residues in contact with SER 106 (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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86A HIS* 3.2 31.1 + - - -
88A LEU 3.1 12.7 + - - -
89A GLY 3.0 15.3 + - - -
90A ILE* 4.2 0.4 - - - +
91A SER 4.6 0.2 - - - +
105A ALA* 1.3 74.4 - - - +
107A ASP* 1.3 64.5 + - - +
108A ASP* 3.0 25.4 + - - -
109A LYS* 3.1 8.1 + - - -
110A THR 3.1 7.3 + - - -
132A VAL* 3.0 27.2 + - - +
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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