Contacts of the strand formed by residues 24 - 34 (chain B) in PDB entry 5V1Y
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 24 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B TYR* 3.4 2.9 - - - +
23B LEU* 1.3 79.1 - - - +
25B GLU* 1.3 67.9 + - - +
26B PHE* 4.4 8.5 - - + -
48B TYR* 3.2 5.1 - - - +
49B ILE* 3.0 57.9 + - + +
120B HIS* 3.8 30.1 - - + +
123B LYS* 4.1 21.8 - - + -
124B VAL* 4.2 12.6 - - + +
127B TYR* 4.3 6.5 - - + -
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Residues in contact with GLU 25 (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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22B TYR* 3.5 27.2 - - + +
24B VAL* 1.3 78.5 - - - +
26B PHE* 1.3 69.3 + - - +
46B LEU* 3.7 21.7 - - + +
47B VAL 3.2 11.4 - - - +
48B TYR* 3.9 9.4 - - + -
120B HIS* 3.7 13.9 + - - -
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Residues in contact with PHE 26 (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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24B VAL* 4.4 6.1 - - + -
25B GLU* 1.3 80.8 - - - +
27B ARG* 1.3 68.3 + - - +
28B ALA* 4.1 3.6 - - + -
46B LEU* 3.5 7.5 - - - -
47B VAL* 2.9 66.5 + - + -
82B PHE* 4.0 25.4 - + - -
107B PHE* 5.7 1.3 - - + -
109B MET* 3.5 34.3 - - + -
111B GLU* 3.6 13.7 - - + +
120B HIS* 3.6 43.3 - + + +
124B VAL* 3.9 21.1 - - + -
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Residues in contact with ARG 27 (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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26B PHE* 1.3 77.3 - - - +
28B ALA* 1.3 61.1 + - - +
45B GLY 3.4 5.2 - - - -
46B LEU* 4.2 10.1 - - + -
64B ARG* 3.6 32.3 - - - +
109B MET* 3.8 2.8 - - - +
110B GLN* 2.9 29.8 + - + -
111B GLU* 2.8 32.8 + - - +
112B PRO* 4.2 13.7 - - - +
941F GLU* 3.1 35.5 + - - +
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Residues in contact with ALA 28 (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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26B PHE* 3.5 13.9 + - + -
27B ARG* 1.3 76.5 - - - +
29B GLY* 1.3 63.7 + - - +
45B GLY* 3.0 18.5 + - - -
47B VAL* 4.0 24.0 - - + -
61B TRP* 2.9 20.0 + - - -
107B PHE* 4.4 4.9 - - + -
108B TRP 3.1 18.6 - - - +
109B MET* 4.2 1.8 - - - -
110B GLN* 3.1 9.3 + - - +
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Residues in contact with GLY 29 (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 ALA* 1.3 73.5 - - - +
30B LYS* 1.3 64.6 + - - -
43B ARG 3.8 8.3 - - - -
61B TRP* 4.1 3.1 - - - -
107B PHE* 3.1 11.6 - - - +
108B TRP* 2.8 41.2 + - - -
110B GLN* 3.2 20.7 - - - -
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Residues in contact with LYS 30 (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 GLY* 1.3 72.2 - - - -
31B MET* 1.3 67.2 + - - +
41B ASP* 2.8 37.6 + - + +
43B ARG* 3.8 8.7 + - - +
61B TRP* 3.6 37.3 - - + +
70B GLU* 2.8 28.9 + - - +
71B ASP* 2.8 35.3 + - - +
106B PHE 3.4 6.7 - - - +
107B PHE* 3.9 15.9 - - + -
108B TRP* 3.2 10.8 + - - +
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Residues in contact with MET 31 (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 LYS* 1.3 83.1 - - - +
32B SER* 1.3 61.8 + - - +
38B VAL* 3.7 28.3 - - + +
39B THR 3.3 13.0 - - - +
40B PRO* 3.7 31.2 - - + -
41B ASP* 4.1 2.9 - - - +
93B VAL* 3.7 36.8 - - - -
105B LEU* 5.6 0.2 - - - -
106B PHE* 3.0 30.2 + - + +
107B PHE 4.6 0.2 - - - +
108B TRP* 3.6 18.8 - - + +
945F PRO* 3.9 16.2 - - + -
946F GLU 4.8 0.7 - - - +
948F PHE* 3.9 11.9 - - + -
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Residues in contact with SER 32 (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 MET* 1.3 75.3 - - - +
33B LEU* 1.3 61.3 + - - +
34B LYS* 3.1 25.2 + - - -
37B THR 3.6 1.6 - - - +
38B VAL* 3.3 6.2 - - - -
39B THR* 2.9 37.4 + - - +
106B PHE* 5.0 2.2 - - - -
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Residues in contact with LEU 33 (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 SER* 1.3 74.6 - - - +
34B LYS* 1.3 66.8 + - - +
35B GLY 3.5 24.7 - - - +
36B THR* 3.8 4.5 - - - +
37B THR 3.5 24.2 - - - +
38B VAL* 3.7 15.0 - - + +
104B ARG* 5.3 9.2 - - + +
106B PHE* 3.9 27.6 - - + -
950F TYR* 4.3 19.5 - - + +
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Residues in contact with LYS 34 (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 SER* 3.1 34.0 + - - +
33B LEU* 1.3 78.6 - - - +
35B GLY* 1.3 66.5 - - - +
36B THR 3.1 0.2 + - - -
37B THR* 3.0 29.1 + - - +
39B THR* 4.3 17.0 - - - +
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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