Contacts of the strand formed by residues 37 - 48 (chain B) in PDB entry 1HB0
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 SER 37 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B SER* 1.3 138.0 + - - +
38B TRP* 1.3 69.8 + - - +
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Residues in contact with TRP 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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34B GLN* 3.7 11.2 - - - +
35B TYR 3.5 5.4 - - - -
36B SER* 3.4 47.8 - - + +
37B SER* 1.3 84.9 - - - +
39B ALA* 1.3 62.2 + - - +
64B THR* 3.6 31.9 - - + -
65B ARG* 3.4 80.3 - - + +
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Residues in contact with ALA 39 (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 GLN* 3.1 4.9 - - - -
35B TYR* 2.9 63.5 + - + +
36B SER* 4.8 6.3 - - + -
37B SER 4.3 0.4 + - - -
38B TRP* 1.3 74.8 - - - +
40B HIS* 1.3 66.3 + - - +
41B THR 3.5 0.2 + - - -
151B LEU* 6.5 0.2 - - + -
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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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32B SER* 2.8 23.8 + - - +
33B LEU 3.8 4.3 - - - -
34B GLN* 4.0 9.3 - - - +
35B TYR* 4.5 2.3 - - - -
39B ALA* 1.3 77.0 - - - +
41B THR* 1.3 63.7 + - - +
42B CYS 3.1 27.6 + - - -
43B GLY* 4.2 1.1 - - - -
73B LEU* 3.8 23.2 - - + +
141B TRP* 3.6 35.5 - + + +
151B LEU* 3.9 37.6 - - + +
193B GLY 2.9 24.9 + - - -
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Residues in contact with THR 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 2.8 28.1 + - + +
34B GLN* 4.4 1.3 - - - -
35B TYR* 3.5 31.6 - - + -
39B ALA 3.5 0.4 + - - -
40B HIS* 1.3 80.5 - - - +
42B CYS* 1.3 82.7 + - + +
58B CYS 4.9 3.5 + - - +
63B LEU* 6.0 0.6 - - + +
65B PHE* 4.3 14.1 - - + -
151B LEU* 6.3 0.2 - - - -
193B GLY* 3.5 17.0 + - - -
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Residues in contact with CYS 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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33B LEU* 2.7 41.4 + - + -
40B HIS* 3.1 14.4 + - - -
41B THR* 1.3 97.8 - - - +
43B GLY* 1.3 61.7 + - - +
57B HIS* 5.0 1.6 - - - -
58B CYS* 2.0 56.1 - - + -
193B GLY 3.6 5.6 - - - -
195B SER* 3.2 13.0 - - - +
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Residues in contact with GLY 43 (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 GLN* 3.6 12.1 - - - -
31B ILE* 3.4 14.4 - - - -
33B LEU* 4.5 1.8 - - - +
40B HIS* 4.5 4.0 - - - -
42B CYS* 1.3 76.3 - - - +
44B GLY* 1.3 57.4 + - - -
54B THR* 3.1 12.8 + - - -
140B GLY* 6.0 1.1 - - - -
141B TRP* 5.4 0.2 - - - -
193B GLY 3.7 5.3 + - - -
194B ASP* 4.4 2.5 - - - -
195B SER 2.8 11.1 + - - +
196B GLY 3.1 11.6 - - - -
197B GLY* 3.5 10.8 - - - -
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Residues in contact with GLY 44 (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 GLN* 3.6 9.9 + - - +
31B ILE* 3.0 40.4 + - - -
43B GLY* 1.3 74.4 - - - -
45B THR* 1.3 64.4 + - - -
52B VAL* 4.2 2.5 - - - -
53B MET 3.3 6.7 - - - -
54B THR* 4.3 1.6 - - - -
196B GLY 3.2 12.5 + - - -
197B GLY* 3.7 2.8 - - - -
198B PRO* 3.8 2.8 - - - +
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Residues in contact with THR 45 (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 SER* 3.3 22.2 - - - +
44B GLY* 1.3 74.0 - - - -
46B LEU* 1.3 74.4 + - - +
47B ILE* 3.3 9.6 + - + +
52B VAL* 3.3 4.3 - - - +
53B MET* 2.7 56.9 + - + +
121B GLY* 4.1 4.5 - - - -
123B LEU* 5.0 0.2 - - + -
196B GLY 4.8 0.3 + - - -
197B GLY 4.5 1.0 - - - -
198B PRO* 3.3 29.1 - - - +
209B VAL* 3.9 19.1 - - + +
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Residues in contact with LEU 46 (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 5.2 1.1 - - - +
29B SER* 2.8 15.7 + - - +
31B ILE* 4.1 9.6 - - + +
45B THR* 1.3 71.1 - - - +
47B ILE* 1.3 51.9 + - - +
48B ARG 3.0 24.0 - - - +
51B TRP 3.7 7.9 - - - +
52B VAL* 4.0 15.0 - - + -
68B VAL* 4.5 8.7 - - + -
108B LEU* 4.1 15.5 - - + -
112B VAL* 3.8 14.8 - - + -
114B LEU* 4.1 2.9 - - + -
118B VAL* 3.7 30.3 - - + -
119B GLN 3.8 16.2 - - - +
120B LEU* 3.5 13.7 - - + -
121B GLY* 2.6 34.1 + - - -
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Residues in contact with ILE 47 (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 THR* 3.6 19.1 - - + +
46B LEU* 1.3 78.8 - - - +
48B ARG* 1.3 85.6 + - + +
51B TRP* 3.0 20.3 + - + +
53B MET* 3.9 13.9 - - + +
105B LEU* 3.7 29.6 - - + -
120B LEU* 3.8 16.2 - - - +
121B GLY 4.3 7.7 - - - +
123B LEU* 4.2 28.5 - - + -
238B ILE* 3.9 20.4 - - + -
242B ILE* 4.0 11.9 - - + -
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Residues in contact with ARG 48 (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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46B LEU* 3.0 20.3 - - - +
47B ILE* 1.3 95.2 + - - +
49B GLN* 1.3 64.9 + - - +
50B ASN* 2.9 7.4 + - - +
51B TRP* 3.2 33.8 + - + +
120B LEU* 3.3 16.8 - - - +
123B LEU* 6.1 2.0 - - - +
238B ILE* 5.9 1.0 - - - +
239B ASN* 4.4 13.7 + - - -
242B ILE* 3.7 44.6 - - + +
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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