Contacts of the strand formed by residues 101 - 110 (chain B) in PDB entry 3VKO
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 LYS 101 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B HIS* 3.4 4.7 - - - -
39B VAL* 3.1 25.7 + - - +
96B PRO 4.5 18.2 + - - +
97B PHE* 5.9 0.2 - - - -
98B LYS* 2.9 35.5 + - + +
99B ARG 4.4 1.1 - - - +
100B GLU* 1.3 80.3 - - - +
102B SER* 1.3 76.7 + - - +
103B PHE* 4.2 1.0 - - - -
119B ASN* 4.7 13.9 - - - +
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Residues in contact with SER 102 (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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37B GLY 3.2 8.9 + - - -
38B HIS* 3.4 14.6 - - - +
101B LYS* 1.3 93.3 - - - +
103B PHE* 1.3 64.1 + - - +
119B ASN* 4.0 7.0 + - - +
147B HIS* 4.0 10.7 + - - -
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Residues in contact with PHE 103 (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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35B ILE* 3.9 18.6 - - + -
36B ARG* 3.4 5.3 - - - +
37B GLY* 2.7 47.4 + - - +
38B HIS* 3.7 21.8 - - - -
39B VAL* 3.9 16.6 - - + -
46B PHE* 4.0 13.9 - + - -
97B PHE* 3.7 30.1 - + + -
101B LYS 4.2 0.7 - - - -
102B SER* 1.3 78.1 - - - +
104B GLU* 1.3 62.3 + - - +
105B ILE* 3.9 18.8 - - + -
118B VAL* 4.3 7.2 - - + -
119B ASN* 3.5 11.4 - - - +
144B VAL* 3.6 23.8 - - + -
146B ILE* 4.4 3.1 - - + -
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Residues in contact with GLU 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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34B VAL* 4.0 14.6 - - + +
35B ILE 3.4 3.8 - - - -
36B ARG* 2.5 51.3 + - + +
103B PHE* 1.3 76.4 - - - +
105B ILE* 1.3 61.2 + - - +
106B VAL* 3.8 12.5 + - + +
117B ALA 3.5 1.4 - - - +
118B VAL* 3.4 4.7 - - - -
119B ASN* 3.0 36.9 + - - +
120B GLY 4.7 0.3 + - - -
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Residues in contact with ILE 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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33B ILE 3.6 0.5 - - - +
34B VAL* 3.3 5.7 - - - +
35B ILE* 2.8 48.1 + - + +
46B PHE* 4.7 4.9 - - + -
48B VAL* 4.6 14.6 - - + -
66B PHE* 3.8 16.6 - - + -
97B PHE* 3.6 35.9 - - + -
103B PHE* 3.9 21.1 - - + -
104B GLU* 1.3 73.0 - - - +
106B VAL* 1.3 65.3 + - - +
107B ILE* 3.9 27.1 - - + -
116B VAL* 3.9 15.7 - - + -
117B ALA 3.6 3.4 - - - +
118B VAL* 4.4 2.9 - - + -
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Residues in contact with VAL 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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32B LEU* 4.2 31.9 - - + -
33B ILE 3.5 2.9 - - - -
34B VAL* 4.3 17.5 - - + -
104B GLU* 4.4 20.0 - - - +
105B ILE* 1.3 79.1 - - - +
107B ILE* 1.3 63.5 + - - +
108B MET* 4.7 2.0 - - + +
115B GLN* 3.5 4.2 + - - +
116B VAL* 3.5 3.5 - - - -
117B ALA* 2.8 45.0 + - + +
120B GLY* 5.9 3.8 - - - +
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Residues in contact with ILE 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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31B THR 3.6 1.0 - - - +
32B LEU* 3.2 5.0 - - - -
33B ILE* 2.8 54.6 + - + +
35B ILE* 5.2 1.8 - - + -
48B VAL* 4.3 24.5 - - + -
50B LEU* 4.5 18.6 - - + -
64B PHE* 4.3 16.4 - - + -
66B PHE* 5.4 4.3 - - + -
105B ILE* 3.9 19.7 - - + -
106B VAL* 1.3 75.7 - - - +
108B MET* 1.3 60.9 + - - +
109B VAL* 4.9 1.9 - - + +
114B PHE* 3.8 34.1 - - + -
115B GLN 3.8 2.7 - - - -
116B VAL* 4.4 10.5 - - + +
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Residues in contact with MET 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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30B GLY* 4.8 8.5 - - - -
31B THR 3.3 4.9 - - - +
32B LEU* 3.5 23.8 - - + -
106B VAL* 3.7 1.8 + - + +
107B ILE* 1.3 73.9 - - - +
109B VAL* 1.3 72.3 + - - +
110B LEU* 3.6 24.0 + - + +
114B PHE* 3.5 5.2 - - - -
115B GLN* 2.9 81.1 + - + +
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Residues in contact with VAL 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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27B LEU* 3.7 36.3 - - + +
28B ASP 3.9 9.9 - - - +
29B PRO* 4.3 0.2 - - - -
30B GLY* 2.6 34.5 + - - -
31B THR* 2.8 32.8 + - + +
33B ILE* 5.1 3.6 - - + -
107B ILE* 4.9 6.3 - - + +
108B MET* 1.3 74.0 - - - +
110B LEU* 1.3 70.6 + - - +
113B LYS 4.2 1.3 - - - -
114B PHE* 4.0 27.6 - - + -
128B HIS* 4.2 0.9 - - - +
132B PRO* 4.0 13.5 - - + -
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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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29B PRO* 4.5 7.4 - - + +
30B GLY* 4.9 4.7 - - - +
108B MET* 3.6 36.3 + - + +
109B VAL* 1.3 86.8 - - - +
111B LYS* 1.3 62.4 + - - +
112B ASP* 3.1 4.7 - - - +
113B LYS* 2.8 41.3 + - + +
115B GLN* 4.5 9.0 - - + -
125B LEU* 5.8 0.7 - - + -
128B HIS* 3.0 22.3 + - - -
132B PRO* 4.7 2.1 - - - +
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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