Contacts of the strand formed by residues 107 - 116 (chain B) in PDB entry 2VQ5
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 107 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A HIS* 5.8 4.9 - - + -
82B LYS* 5.7 1.7 - - - -
96B ASP* 2.8 36.7 - - - +
97B MSE 3.1 10.8 - - - +
98B THR* 3.3 18.9 + - - +
99B PHE* 4.7 0.4 - - - -
105B PRO 3.4 1.4 - - - -
106B HIS* 1.3 96.8 + - + +
108B TYR* 1.3 63.5 + - - +
129B GLY* 3.8 3.9 - - - -
130B GLY 3.1 21.1 + - - -
1195B CL 3.4 5.9 - - - +
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Residues in contact with TYR 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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95B LEU 3.8 0.7 - - - +
96B ASP* 3.6 2.4 - - - +
97B MSE 2.9 41.5 + - + -
99B PHE* 3.5 19.8 - + - -
105B PRO* 3.3 39.5 - - + -
107B GLU* 1.3 75.6 - - - +
109B LYS* 1.3 64.1 + - - +
110B GLU* 3.6 37.0 - - + -
126B MSE 3.8 27.8 - - + -
128B GLU 3.2 16.4 - - - +
129B GLY* 3.9 2.0 - - - -
130B GLY* 3.8 7.6 - - - +
131B TYR* 5.3 0.9 - + - -
179B PRO* 4.7 7.1 - - - +
1197B LDP 2.9 28.1 + - - -
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Residues in contact with LYS 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B GLU* 6.0 0.2 - - - -
86B ILE* 4.9 8.5 - - - -
94B ILE* 4.0 19.5 - - + -
95B LEU 3.2 5.4 - - - +
96B ASP* 3.3 36.8 + - + +
108B TYR* 1.3 74.2 - - - +
110B GLU* 1.3 57.5 + - - +
126B MSE 3.5 7.3 - - - +
127B ILE* 2.8 48.1 + - + -
128B GLU* 2.8 48.0 + - + +
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Residues in contact with GLU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B THR 3.9 0.5 - - - +
94B ILE* 3.2 5.4 - - - +
95B LEU* 2.8 43.6 + - + +
97B MSE 4.1 5.9 - - - +
108B TYR* 3.6 33.4 - - + -
109B LYS* 1.3 77.4 - - - +
111B LYS* 1.3 60.7 + - - +
124B VAL* 3.7 24.8 - - + +
125B GLN 3.2 6.1 - - - +
126B MSE 4.2 18.1 + - - +
127B ILE* 4.5 2.5 - - - -
139B TYR* 4.9 0.9 - - - -
141B ASP* 4.0 12.3 - - - +
1197B LDP 3.0 32.9 - - - -
1198B HBA 3.9 1.5 + - - -
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Residues in contact with LYS 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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92B GLY* 3.9 23.6 - - - +
93B THR 3.5 9.6 - - - +
94B ILE* 3.8 23.8 - - + +
110B GLU* 1.3 75.5 - - - +
112B PHE* 1.3 64.4 + - - +
113B ILE* 3.2 28.5 + - + +
124B VAL* 3.3 6.0 - - - -
125B GLN 2.8 32.8 + - - +
127B ILE* 4.0 24.5 - - + -
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Residues in contact with PHE 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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63B TYR 4.9 3.8 - - - -
64B SER* 5.4 8.7 - - - -
65B TRP 5.7 2.2 - - - -
66B PRO* 5.9 0.2 - - + -
89B GLY 3.4 25.4 - - - -
90B GLY* 3.4 22.7 - - - +
91B VAL* 3.6 4.1 - - + -
92B GLY* 2.7 31.7 + - - -
93B THR* 2.9 20.3 + - + +
110B GLU 4.3 0.2 - - - -
111B LYS* 1.3 68.7 - - - +
113B ILE* 1.3 63.7 + - - +
114B LEU 3.6 4.0 - - - -
115B VAL* 3.1 36.8 - - + -
122B LYS* 3.4 44.4 - - + -
123B LYS 3.9 7.6 - - - -
124B VAL* 4.5 6.7 - - + +
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Residues in contact with ILE 113 (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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91B VAL* 3.7 13.5 - - - +
111B LYS* 3.2 31.3 + - + +
112B PHE* 1.3 74.6 - - - +
114B LEU* 1.3 73.1 + - + +
123B LYS* 3.0 14.6 + - + +
125B GLN* 2.8 44.2 - - + +
127B ILE* 5.2 1.1 - - + -
140B MSE 3.9 18.8 - - + -
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Residues in contact with LEU 114 (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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91B VAL* 4.1 3.1 - - - -
112B PHE* 3.6 4.9 - - - -
113B ILE* 1.3 86.2 - - + +
115B VAL* 1.3 90.5 + - - +
116B ASP* 4.3 7.6 - - + +
121B LEU* 4.7 6.3 - - + +
122B LYS* 3.5 4.0 - - - -
123B LYS* 3.0 59.6 + - + +
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Residues in contact with VAL 115 (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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60B TRP* 3.5 27.4 - - + -
64B SER* 4.7 7.2 - - - +
91B VAL* 3.1 20.8 - - + +
112B PHE* 3.1 40.6 - - + -
114B LEU* 1.3 83.4 - - - +
116B ASP* 1.3 61.7 + - - +
117B ASN* 3.6 19.4 + - - +
121B LEU 3.6 2.7 - - - -
122B LYS* 4.9 1.3 - - + -
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Residues in contact with ASP 116 (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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60B TRP* 3.9 1.5 - - - -
114B LEU* 4.3 8.5 - - + +
115B VAL* 1.3 72.7 - - - +
117B ASN* 1.3 57.2 + - - +
118B GLU* 3.2 9.5 + - - +
119B HIS* 2.7 48.0 + - - +
120B ARG 2.8 22.2 + - - -
121B LEU* 2.8 33.6 + - + +
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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