Contacts of the strand formed by residues 37 - 42 (chain B) in PDB entry 6HBU
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 37 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ALA 3.7 2.9 + - - +
36B VAL* 1.3 73.6 - - - +
38B SER* 1.3 57.1 + - - +
39B PHE* 4.2 7.3 - - + -
70B ILE 3.7 0.2 - - - -
71B MET* 2.7 51.9 + - + +
93B LEU* 3.7 42.0 - - + +
106B VAL* 3.8 17.5 - - + -
107B LEU 3.4 3.6 - - - -
108B ILE* 4.2 24.9 - - + +
117B PHE* 5.0 0.9 - - + -
206B ILE* 4.1 15.5 - - + -
208B PHE* 3.6 30.3 - - + -
237B THR* 5.5 0.9 - - + -
239B ILE* 4.7 4.7 - - + -
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Residues in contact with SER 38 (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 VAL 3.6 2.7 + - - -
37B LEU* 1.3 74.0 - - - +
39B PHE* 1.3 59.7 + - - +
40B HIS* 5.6 0.7 - - - -
69B GLY 3.6 5.4 - - - -
70B ILE* 4.2 6.3 - - - +
105B ASP 4.0 0.9 - - - +
106B VAL* 3.4 2.7 - - - +
107B LEU* 2.7 60.4 + - - +
110B GLY 5.0 1.2 + - - -
349B LEU* 3.9 15.9 - - - +
352B LEU* 3.8 32.4 - - - +
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Residues in contact with PHE 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 4.2 5.4 - - + -
38B SER* 1.3 77.0 - - - +
40B HIS* 1.3 61.4 + - - +
42B ILE* 3.7 18.2 - - + -
67B ILE* 3.5 35.4 - - + -
68B ASN* 3.6 2.3 - - - -
69B GLY* 3.0 67.2 + - - +
71B MET* 3.7 37.5 - - + -
89B LEU* 4.4 12.8 - - + -
93B LEU* 3.8 22.4 - - + -
105B ASP 3.5 4.0 - - - -
106B VAL* 3.9 16.6 - - + +
257B THR* 5.5 2.5 - - + -
264B LEU* 6.1 0.7 - - + -
267B HIS* 5.0 3.4 - + - -
349B LEU* 3.9 3.5 - - - +
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Residues in contact with HIS 40 (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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38B SER 5.6 0.2 - - - +
39B PHE* 1.3 75.6 - - - +
41B ASN* 1.3 93.4 + - - +
42B ILE* 3.3 2.5 - - - +
68B ASN* 3.4 13.0 - - - -
104B GLY* 3.6 0.2 - - - -
105B ASP* 2.9 48.6 + - - +
107B LEU* 5.5 3.6 - - + -
346B LYS* 3.1 21.6 + - - -
349B LEU* 3.9 31.9 + - + +
350B HIS* 4.0 25.6 + + - -
353B SER* 5.0 10.2 + - - -
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Residues in contact with ASN 41 (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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40B HIS* 1.3 100.8 + - + +
42B ILE* 1.3 63.2 + - - +
43B CYS* 3.3 7.0 + - - -
66B ASN* 4.6 15.2 + - - +
67B ILE 3.6 4.0 + - - +
68B ASN* 2.4 23.0 + - - +
103B SER 3.0 24.2 - - - +
104B GLY* 3.4 0.8 - - - -
346B LYS* 3.9 12.9 + - - +
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Residues in contact with ILE 42 (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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39B PHE* 3.7 24.0 - - + -
40B HIS 3.9 3.6 - - - +
41B ASN* 1.3 74.1 - - - +
43B CYS* 1.3 70.4 + - - +
64B LEU* 3.8 19.2 - - + +
65B SER 2.8 21.3 - - - +
67B ILE* 3.2 23.8 + - + +
89B LEU* 4.6 4.9 - - + -
92B VAL* 3.7 25.1 - - + -
93B LEU* 5.3 0.9 - - + -
102B LEU* 4.6 3.1 - - + -
104B GLY* 3.9 6.3 - - - +
105B ASP 3.6 35.2 - - - +
106B VAL* 3.9 16.8 - - + -
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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