Contacts of the strand formed by residues 103 - 112 (chain B) in PDB entry 1VWJ
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 103 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21B TRP* 3.9 1.3 - - - -
95B GLN 3.9 0.7 - - - +
96B TYR* 3.6 2.8 - - - -
97B VAL* 2.9 37.1 + - + +
101B GLU* 2.9 52.4 + - - +
102B ALA* 1.3 89.3 + - - +
104B ILE* 1.3 67.1 + - - +
105B ASN* 4.0 20.2 - - - +
129B THR* 4.2 12.5 - - + +
130B PHE 3.3 17.0 - - - +
131B THR* 3.6 32.4 + - - +
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Residues in contact with ILE 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ILE* 4.8 5.6 - - + -
21B TRP* 3.6 43.3 - - + +
29B PHE* 4.1 20.4 - - + -
73B LEU* 4.1 29.6 - - + -
75B TRP* 4.3 6.7 - - + -
95B GLN 3.3 9.6 - - - +
96B TYR* 4.1 11.4 - - + -
103B ARG* 1.3 77.2 - - - +
105B ASN* 1.3 61.6 + - - +
106B THR* 3.7 21.8 - - + -
129B THR* 3.4 2.6 - - - -
130B PHE* 2.9 41.2 + - + -
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Residues in contact with ASN 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B GLY* 3.0 22.7 - - - -
95B GLN* 3.0 14.1 + - + +
97B VAL* 4.4 17.8 - - - +
103B ARG* 4.2 13.9 - - - +
104B ILE* 1.3 74.4 - - - +
106B THR* 1.3 60.5 + - - +
128B ASP 3.9 2.5 - - - -
129B THR* 3.1 32.0 + - - +
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Residues in contact with THR 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B TRP* 3.9 20.9 - - + -
92B TRP* 3.3 27.6 - - + -
93B SER 3.4 13.0 - - - +
94B GLY* 4.3 3.6 - - - -
104B ILE* 3.7 22.4 - - + -
105B ASN* 1.3 80.2 - - - +
107B GLN* 1.3 67.1 - - - +
127B HIS* 3.2 9.7 - - - +
128B ASP 2.8 46.0 + - - +
130B PHE* 3.8 6.1 - - + -
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Residues in contact with GLN 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B TRP* 3.6 0.5 - - - -
93B SER 3.0 30.1 + - - +
106B THR* 1.3 79.3 - - - +
108B TRP* 1.3 61.5 + - - +
125B VAL* 4.6 11.0 - - + +
126B GLY* 3.2 25.9 + - - -
127B HIS* 3.7 19.1 - - - +
109D LEU* 3.5 21.4 - - + +
123D THR* 4.6 24.9 - - + +
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Residues in contact with TRP 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B LEU* 6.3 2.7 - - + -
90B THR* 4.0 5.6 - - + -
91B THR 3.2 13.9 - - - +
92B TRP* 3.7 20.0 - + + +
107B GLN* 1.3 75.1 - - - +
109B LEU* 1.3 66.4 + - - +
110B LEU* 3.5 33.2 - - + -
124B LEU* 3.8 24.7 - - + -
125B VAL* 3.3 15.4 - - - +
126B GLY* 2.9 52.6 + - - -
127B HIS* 3.3 15.0 - - - +
128B ASP* 3.5 34.3 + - - -
109D LEU* 4.1 1.8 - - - -
5M GLN* 3.2 23.6 - - - -
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Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B THR* 3.2 2.6 - - - -
91B THR* 3.0 34.0 + - - +
108B TRP* 1.3 81.5 - - - +
110B LEU* 1.3 59.8 + - - +
123B THR* 4.1 13.0 - - + -
124B LEU 3.3 7.9 - - - +
125B VAL* 4.0 19.7 - - + -
91D THR 4.9 0.4 - - - +
93D SER* 3.3 22.8 + - - -
107D GLN* 3.6 43.3 - - + +
108D TRP* 4.0 4.0 - - - +
109D LEU* 3.8 29.6 - - + +
125D VAL* 5.4 5.4 - - + -
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Residues in contact with LEU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B TRP* 4.0 1.6 - - - +
88B SER* 3.8 25.1 - - - -
89B ALA 3.5 6.5 - - - +
90B THR* 3.2 19.7 - - - +
108B TRP* 3.5 18.8 - - + -
109B LEU* 1.3 71.9 - - - +
111B THR* 1.3 63.5 + - - +
112B SER* 4.7 5.1 + - - +
122B SER 3.5 2.1 - - - +
123B THR* 3.3 2.3 - - - -
124B LEU* 2.8 55.9 + - + +
3M HIS* 4.0 27.8 - - + +
5M GLN* 3.7 17.5 - - + +
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Residues in contact with THR 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B SER* 3.2 3.9 - - - -
89B ALA 2.9 33.3 + - - -
110B LEU* 1.3 71.6 - - - +
112B SER* 1.3 73.4 + - - +
122B SER* 3.4 10.1 - - - +
123B THR* 3.4 27.6 + - - +
72D ALA* 3.6 4.0 - - - +
73D LEU 5.1 0.9 - - - -
93D SER* 2.8 29.7 + - - -
94D GLY* 3.5 34.5 - - - +
95D GLN* 4.4 5.4 - - + +
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Residues in contact with SER 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B ALA 5.6 0.4 - - - -
87B HIS 3.5 8.3 - - - -
88B SER* 3.7 11.5 - - - -
110B LEU* 4.7 6.1 - - - +
111B THR* 1.3 87.5 - - - +
113B GLY* 1.3 68.7 + - - +
114B THR* 3.4 16.6 + - - +
122B SER* 3.1 16.8 + - - -
72D ALA* 4.4 1.6 - - - -
95D GLN* 3.9 2.9 - - - +
3M HIS* 6.0 0.7 - - - -
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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