Contacts of the strand formed by residues 111 - 124 (chain B) in PDB entry 1VLP
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 111 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B SER 5.0 1.2 + - - -
42B GLN* 2.9 46.9 + - - +
44B THR* 4.9 9.1 - - + +
108B ILE* 2.9 38.2 + - + +
109B GLU 4.5 1.3 - - - +
110B GLY* 1.3 85.0 - - - +
112B PRO* 1.3 68.8 - - - +
114B HIS* 2.9 39.5 + - + +
502B EDO 3.2 32.3 + - - +
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Residues in contact with PRO 112 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333A GLU* 4.0 17.3 - - - +
107B GLU* 3.4 17.7 - - + +
108B ILE 3.8 1.1 - - - +
110B GLY* 3.4 7.6 - - - +
111B LYS* 1.3 93.1 - - - +
113B THR* 1.3 76.6 + - + +
114B HIS* 3.3 5.9 + - - -
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Residues in contact with THR 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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45B PHE 4.0 3.6 - - - +
46B ASN* 4.2 10.4 - - - +
47B LYS* 5.0 1.7 + - - +
107B GLU* 2.7 17.7 + - - +
112B PRO* 1.3 79.8 + - + +
114B HIS* 1.3 74.2 + - - +
115B TYR* 3.7 20.5 - - - -
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Residues in contact with HIS 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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44B THR* 3.3 27.5 + - + +
45B PHE 3.5 5.6 + - - -
46B ASN* 5.9 2.9 - - + +
107B GLU* 3.5 4.3 - - - +
108B ILE* 2.8 34.5 + - + +
111B LYS* 2.9 30.2 + - + +
112B PRO 3.3 22.7 - - - -
113B THR* 1.3 92.3 + - - +
115B TYR* 1.3 57.6 - - - +
147B VAL* 6.4 0.2 - - - +
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Residues in contact with TYR 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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44B THR* 3.7 7.3 - - - -
45B PHE* 2.8 42.7 + - + +
46B ASN* 4.3 3.4 - - - -
47B LYS* 3.9 34.0 - - + +
50B ILE* 3.6 26.2 - - + -
105B SER* 4.0 15.9 - - - -
106B GLU* 3.4 6.7 - - - +
107B GLU* 3.4 47.3 + - + -
108B ILE* 3.8 5.1 - - - +
113B THR* 3.7 24.7 - - - -
114B HIS* 1.3 76.7 - - - +
116B LYS* 1.3 63.9 + - - +
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Residues in contact with LYS 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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105B SER* 3.2 5.0 - - - -
106B GLU* 2.9 58.2 + - + +
108B ILE* 3.8 16.4 - - + +
115B TYR* 1.3 74.3 - - - +
117B LEU* 1.3 67.2 + - - +
118B LYS* 5.5 0.2 - - - +
501B CL 3.8 11.9 - - + -
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Residues in contact with LEU 117 (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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36B TYR* 3.6 33.5 - - + +
45B PHE* 3.7 43.1 - - + -
50B ILE* 3.8 31.9 - - + -
53B LEU* 4.0 20.0 - - + -
103B PHE* 4.0 20.0 - - + -
104B THR 3.7 2.5 - - - -
105B SER* 4.3 1.1 - - - -
116B LYS* 1.3 85.2 - - - +
118B LYS* 1.3 61.9 + - - +
119B ILE* 4.2 5.4 - - + -
139B ILE* 4.3 9.4 - - + -
501B CL 3.3 4.4 - - + +
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Residues in contact with LYS 118 (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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372A GLU* 2.5 34.1 + - - +
35B LYS* 6.1 6.5 - - + +
36B TYR* 4.9 1.1 - - - -
102B SER* 3.5 5.3 - - - +
103B PHE* 3.4 1.2 - - - -
104B THR* 2.8 57.1 + - - +
105B SER* 5.5 0.9 - - - -
116B LYS 5.5 0.2 - - - +
117B LEU* 1.3 73.2 - - - +
119B ILE* 1.3 70.2 + - - +
120B LEU* 4.0 26.8 - - + +
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Residues in contact with ILE 119 (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 TYR 4.0 0.2 - - - +
35B LYS* 3.6 4.7 - - - +
36B TYR* 2.9 52.0 + - + +
57B PHE* 3.8 21.1 - - + -
101B ILE* 4.3 15.9 - - + -
102B SER 3.4 2.2 - - - -
103B PHE* 3.5 21.1 - - + -
117B LEU* 4.6 5.2 - - + -
118B LYS* 1.3 82.8 - - - +
120B LEU* 1.3 67.0 + - - +
121B VAL* 4.1 20.9 - - + -
135B LEU* 4.5 8.5 - - + -
139B ILE* 3.7 30.7 - - + -
378B ILE* 5.1 3.4 - - + -
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Residues in contact with LEU 120 (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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42A GLN* 6.5 0.7 - - + -
33B THR* 4.1 18.2 - - + -
34B TYR 3.4 4.9 - - - +
35B LYS* 3.8 38.6 - - + -
100B GLN 3.5 1.4 - - - +
101B ILE* 3.6 1.2 - - - +
102B SER* 2.7 51.2 + - - +
118B LYS* 4.0 27.6 - - + +
119B ILE* 1.3 75.4 - - - +
121B VAL* 1.3 61.4 + - - +
122B SER* 4.1 3.1 - - - +
381B LEU* 4.7 4.3 - - + -
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Residues in contact with VAL 121 (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 VAL 3.9 0.7 - - - +
33B THR* 3.3 2.0 - - - -
34B TYR* 2.8 53.0 + - + +
100B GLN* 3.2 12.1 - - + +
101B ILE* 4.4 5.6 - - + -
119B ILE* 4.1 9.4 - - + -
120B LEU* 1.3 75.5 - - - +
122B SER* 1.3 61.4 + - - +
128B THR* 4.1 11.4 - - + +
131B TYR* 3.5 40.6 - - + -
135B LEU* 3.8 27.4 - - + -
378B ILE* 5.0 6.5 - - + -
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Residues in contact with SER 122 (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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42A GLN* 4.2 10.5 + - - -
32B VAL 3.2 6.8 + - - -
33B THR* 2.8 27.4 + - - -
99B GLU 4.4 1.9 - - - +
100B GLN* 2.9 35.2 + - - +
120B LEU* 5.3 3.1 - - - -
121B VAL* 1.3 75.0 - - - +
123B GLY* 1.3 59.5 + - - +
128B THR* 3.6 5.8 - - - -
503B EDO 3.5 9.4 - - - -
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Residues in contact with GLY 123 (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* 4.1 10.8 - - - -
32B VAL* 2.8 30.9 + - - +
100B GLN* 4.3 6.3 - - - -
122B SER* 1.3 76.9 + - - +
124B SER* 1.3 70.3 + - - +
128B THR* 3.5 4.1 - - - +
503B EDO 5.0 0.6 - - - -
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Residues in contact with SER 124 (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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28B PRO 3.1 24.6 + - - -
29B ASP* 4.6 1.9 - - - -
30B VAL 3.5 8.4 + - - -
31B THR* 4.3 6.9 - - - +
100B GLN* 5.4 0.2 + - - -
123B GLY* 1.3 70.2 - - - -
125B TRP* 1.3 67.4 + - - +
126B LYS* 3.6 12.7 + - - +
127B ASP* 3.1 39.6 + - - +
128B THR* 2.9 15.4 + - - +
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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