Contacts of the strand formed by residues 95 - 101 (chain H) in PDB entry 1BEY
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 95 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38H ARG* 3.4 2.8 - - - -
39H GLN* 3.0 41.8 + - + +
94H ALA* 1.3 74.3 - - - +
96H TYR* 1.3 61.2 + - - +
97H TYR* 3.4 43.9 + - + +
114H GLY* 5.1 2.2 - - - -
115H SER 3.8 15.0 - - - +
116H LEU* 3.5 27.1 - - + +
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Residues in contact with TYR 96 (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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6H GLU* 3.6 19.8 - - - +
18H LEU* 3.0 27.4 - - + -
20H LEU* 3.5 22.9 - - + -
36H TRP* 4.4 8.7 - + + -
37H VAL 3.5 2.7 - - - -
38H ARG* 3.0 64.0 + - + -
48H ILE* 3.4 18.2 - - + -
83H LEU* 4.7 7.4 - - + -
85H LEU* 3.0 15.3 - - + +
92H ASP* 3.6 18.7 + - - +
94H ALA* 4.0 6.0 - - + -
95H VAL* 1.3 73.4 - - - +
97H TYR* 1.3 60.0 + - - +
115H SER* 3.3 17.9 + - - +
117H VAL* 3.4 23.3 - - + -
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Residues in contact with TYR 97 (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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6H GLU* 3.5 2.5 - - - -
36H TRP* 3.1 8.7 - - - -
37H VAL* 2.4 50.2 + - + +
39H GLN* 4.4 4.7 + - + -
45H LEU* 3.8 17.3 - - + -
95H VAL* 3.4 32.9 - - + +
96H TYR* 1.3 76.8 - - - +
98H CYS* 1.3 59.9 + - - +
111H TRP* 3.4 35.4 - + + -
112H GLY 5.0 2.7 - - - +
113H GLN 2.9 31.2 - - - -
114H GLY* 4.2 4.3 - - - -
38L GLN* 3.9 6.1 + - - -
42L LYS 2.9 23.9 + - - -
43L ALA* 3.3 17.6 - - + -
44L PRO* 3.4 12.6 - - + -
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Residues in contact with CYS 98 (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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4H LEU* 3.5 17.2 - - - +
6H GLU* 2.6 34.2 + - - +
22H CYS* 2.0 51.8 - - + -
35H ASN 3.8 4.0 - - - -
36H TRP* 3.7 8.5 - - + -
81H PHE* 3.7 15.7 - - + -
97H TYR* 1.3 74.4 - - - +
99H ALA* 1.3 61.7 + - - +
111H TRP* 4.6 0.2 - - - -
112H GLY 3.3 14.9 + - - +
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Residues in contact with ALA 99 (chain H).
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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34H MET* 3.8 4.8 - - - +
35H ASN* 2.7 32.5 + - - +
36H TRP* 4.6 0.4 - - - +
37H VAL* 4.5 1.6 - - + -
97H TYR 3.8 3.4 + - - -
98H CYS* 1.3 74.9 - - - +
100H ARG* 1.3 60.3 + - - +
108H PHE* 3.3 34.5 - - + -
110H TYR 3.3 7.6 - - - +
111H TRP* 3.8 30.9 - - + +
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Residues in contact with ARG 100 (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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2H VAL* 4.2 5.7 - - - +
4H LEU* 3.8 8.1 - - + -
27H PHE* 3.2 43.7 - - + +
32H PHE* 3.6 45.4 - - + -
33H TYR 3.8 2.5 - - - +
34H MET* 3.4 16.8 - - - -
99H ALA* 1.3 72.0 - - - +
101H GLU* 1.3 67.8 + - - +
102H GLY 3.0 3.3 + - - -
108H PHE* 4.6 0.2 - - - -
109H ASP* 2.5 49.0 + - - +
110H TYR* 2.8 61.1 + - - +
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Residues in contact with GLU 101 (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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32H PHE* 3.0 18.0 - - - -
33H TYR* 2.8 59.9 + - + +
35H ASN* 3.4 12.7 + - - +
50H PHE* 3.6 6.6 - - - -
99H ALA 3.8 3.6 + - - -
100H ARG* 1.3 70.4 - - - +
102H GLY* 1.3 61.3 + - - +
106H ALA* 3.5 21.7 - - + +
107H PRO* 3.4 9.1 - - + +
108H PHE 3.7 10.8 - - - +
91L HIS* 5.9 0.2 - - - -
96L ARG* 2.3 45.2 + - - -
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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