Contacts of the strand formed by residues 33 - 39 (chain H) in PDB entry 2W3S
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 LEU 33 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31H ASN 3.7 0.4 - - - +
32H THR* 1.3 79.0 - - - +
34H HIS* 1.3 66.4 + - - +
62H ILE* 3.9 30.1 - - + -
102H ALA* 4.4 7.4 - - + -
103H ALA 3.7 7.9 - - - +
104H THR* 4.1 14.8 - - + -
249H THR* 3.6 38.6 - - + +
251H ARG* 3.4 47.8 - - + +
252H PRO 2.8 12.0 + - - +
253H CYS* 4.2 11.4 - - - -
254H LYS 2.9 24.7 + - - -
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Residues in contact with HIS 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H ASP* 5.6 0.4 - - - -
32H THR* 3.8 20.3 + - + +
33H LEU* 1.3 84.2 + - - +
35H LEU* 1.3 62.5 + - - +
102H ALA* 3.6 0.2 - - - -
103H ALA 2.8 31.8 + - - +
104H THR 4.1 4.7 - - - -
105H SER* 3.5 18.4 - - - -
106H HIS* 3.5 38.0 + - + +
109H ALA* 3.4 9.6 - - - +
254H LYS* 3.4 42.1 + - + +
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Residues in contact with LEU 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34H HIS* 1.3 76.3 - - - +
36H ALA* 1.3 66.6 + - - +
100H LEU* 3.7 19.1 - - + -
101H VAL 3.0 8.3 - - - +
102H ALA* 3.6 28.7 - - + +
106H HIS* 4.6 12.5 - - - -
109H ALA* 3.7 4.7 - - - +
241H ALA* 3.3 37.5 - - + +
242H CYS* 3.7 10.1 - - - +
245H ALA* 3.9 13.9 - - + -
253H CYS* 4.0 12.8 - - + -
254H LYS 3.0 18.7 + - - +
255H MET* 3.7 23.7 - - + +
256H ARG 5.3 1.0 + - - +
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Residues in contact with ALA 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H LEU* 1.3 78.9 - - - +
37H PHE* 1.3 63.3 + - - +
38H GLY 3.7 0.3 + - - -
100H LEU* 3.5 3.1 - - - +
101H VAL* 2.8 42.3 + - - +
106H HIS* 6.0 0.2 - - + -
109H ALA* 3.5 30.7 - - + +
110H ARG* 4.1 12.8 - - + +
113H ALA* 4.5 4.4 - - + +
255H MET* 3.6 11.2 - - - +
261H ASP* 5.4 6.3 - - - +
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Residues in contact with PHE 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H ALA* 1.3 72.7 - - - +
38H GLY* 1.3 60.7 + - - +
39H LEU* 3.4 26.1 + - + +
85H VAL* 4.4 7.2 - - + -
86H LEU* 3.8 19.5 - - + -
97H PRO* 3.6 22.7 - - + -
99H PHE 3.3 12.1 - - - -
100H LEU* 3.6 21.1 - - + -
113H ALA* 3.5 14.6 - - - +
237H HIS* 3.8 31.9 - - + -
241H ALA* 3.8 10.1 - - + -
255H MET* 3.5 23.4 - - + +
257H TYR* 3.7 28.5 - + - -
261H ASP* 4.8 9.7 + - - +
265H ILE* 4.4 7.2 - - + -
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Residues in contact with GLY 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H ALA 3.7 1.4 + - - -
37H PHE* 1.3 71.9 - - - +
39H LEU* 1.3 61.6 + - - -
97H PRO* 3.3 4.9 - - - +
98H ILE* 2.8 27.9 + - - -
99H PHE* 2.6 51.6 + - - -
113H ALA 4.1 7.6 - - - -
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Residues in contact with LEU 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H PHE* 3.4 35.6 + - + +
38H GLY* 1.3 76.2 - - - +
40H SER* 1.3 65.0 + - - +
41H THR* 3.5 8.7 + - - +
95H GLY* 3.6 24.0 - - - +
96H GLN 3.5 1.3 - - - -
97H PRO* 3.7 7.9 - - + -
98H ILE* 4.3 4.2 - - - +
99H PHE* 4.8 0.4 - - - -
113H ALA 5.1 1.0 + - - -
118H ILE* 4.5 6.1 - - - +
120H TYR* 4.1 4.5 + - - -
261H ASP* 4.9 10.5 - - - +
264H VAL* 3.7 22.0 - - + -
265H ILE* 3.5 31.6 - - + -
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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