Contacts of the strand formed by residues 94 - 101 (chain A) in PDB entry 3VY7
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 VAL 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A ILE* 5.4 6.5 - - + -
52A LEU* 5.4 3.1 - - + -
88A LEU* 4.4 20.8 - - + +
93A SER* 1.3 72.3 - - - +
95A ILE* 1.3 59.8 + - - +
96A GLN 3.3 25.6 - - - +
97A VAL* 3.7 17.9 - - + -
110A PHE* 4.1 24.5 - - + -
111A VAL 3.4 7.9 - - - +
112A THR* 4.2 8.1 - - + +
138A VAL* 3.5 5.3 - - - +
139A LEU* 2.8 52.8 + - + +
157A TRP* 3.6 2.1 - - + -
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Residues in contact with ILE 95 (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 SER 4.2 0.9 - - - +
94A VAL* 1.3 76.8 - - - +
96A GLN* 1.3 82.3 + - - +
111A VAL* 2.8 23.7 + - + +
112A THR 3.9 19.5 - - - +
113A ASP* 4.0 24.7 - - + +
132A PRO* 3.1 23.6 - - + +
137A THR 4.7 4.7 - - - +
138A VAL* 4.2 19.3 - - + +
157A TRP* 3.7 8.3 - - - -
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Residues in contact with GLN 96 (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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94A VAL* 3.3 3.2 - - - +
95A ILE* 1.3 100.7 - - + +
97A VAL* 1.3 70.4 + - - +
98A SER 4.3 0.2 - - - -
111A VAL* 2.9 57.5 + - + +
117A TYR* 5.6 2.6 + - - -
129A ASN* 5.1 8.5 + - - +
130A ALA 3.5 8.3 - - - +
131A VAL* 3.7 23.0 - - + +
157A TRP* 3.8 2.4 - - - -
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Residues in contact with VAL 97 (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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94A VAL* 3.7 17.9 - - + -
96A GLN* 1.3 80.6 - - - +
98A SER* 1.3 70.9 + - - +
108A LEU* 4.1 17.9 - - + -
109A VAL 3.2 10.8 - - - +
110A PHE* 3.9 17.0 - - + -
128A PHE* 3.8 3.9 - - + -
129A ASN* 5.6 0.4 - - - -
130A ALA* 2.7 39.2 + - + +
139A LEU* 4.2 2.7 - - + -
155A LEU* 3.9 42.2 - - + -
157A TRP* 3.9 7.8 - - + -
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Residues in contact with SER 98 (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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96A GLN* 5.5 0.4 - - - +
97A VAL* 1.3 80.3 - - - +
99A GLY* 1.3 59.0 + - - +
108A LEU* 3.5 3.8 - - - -
109A VAL* 2.8 52.0 + - - +
111A VAL* 5.6 3.9 - - - +
128A PHE* 3.3 19.2 - - - -
129A ASN* 4.1 18.2 - - - -
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Residues in contact with GLY 99 (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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98A SER* 1.3 79.7 - - - +
100A LYS* 1.3 72.7 + - - +
107A LYS* 3.1 21.1 - - - -
108A LEU* 4.2 0.7 - - - -
109A VAL* 5.7 0.4 - - - -
127A SER* 3.2 2.9 - - - -
128A PHE* 3.0 40.4 + - - +
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Residues in contact with LYS 100 (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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99A GLY* 1.3 79.5 - - - +
101A TYR* 1.3 64.6 + - - +
105A LEU* 3.7 3.7 - - - +
106A LYS* 2.8 22.8 + - - -
107A LYS* 3.1 29.0 + - + +
123A ASP* 3.1 28.3 + - - +
124A SER* 3.3 40.6 - - - +
125A GLY 4.0 9.3 + - - +
126A THR 3.0 9.6 - - - +
127A SER* 4.0 19.6 - - - -
128A PHE* 3.8 2.4 - - - -
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Residues in contact with TYR 101 (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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29A GLU 5.6 0.3 + - - -
30A TYR* 4.0 18.3 - + + -
31A GLY* 3.6 35.0 - - - -
100A LYS* 1.3 75.2 - - - +
102A LYS* 1.3 75.3 + - - +
104A TYR 3.4 14.6 - - - +
105A LEU* 3.9 11.9 - - + -
106A LYS* 4.0 6.9 - - - +
124A SER 4.5 0.2 + - - -
125A GLY* 3.6 3.1 - - - -
126A THR* 2.8 69.6 + - + +
127A SER 5.4 0.2 + - - -
128A PHE* 3.8 29.4 - + + -
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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