Contacts of the strand formed by residues 37 - 42 (chain B) in PDB entry 1HPL
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 ARG 37 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412A LEU* 6.0 2.0 - - - -
439A ARG* 3.2 20.3 - - - +
440A GLU* 5.9 1.4 + - - -
35B ASN* 3.6 35.2 - - - +
36B THR* 1.3 75.8 - - - +
38B PHE* 1.3 61.2 + - - +
39B LEU* 3.4 33.3 - - + +
49B PHE* 3.8 12.7 - - - -
51B GLU* 3.0 41.1 + - - +
103B CYS 3.5 3.3 - - - +
104B VAL* 3.5 5.2 - - - +
105B ASP* 2.9 56.2 + - + +
107B LYS* 5.4 2.4 - - - +
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Residues in contact with PHE 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 THR* 4.1 14.6 - - + -
37B ARG* 1.3 75.2 - - - +
39B LEU* 1.3 60.2 + - - +
40B LEU 3.7 0.6 + - - -
50B GLN 3.7 0.7 - - - +
51B GLU* 3.4 5.3 + - - +
52B ILE* 2.9 60.6 + - + +
53B VAL* 4.9 8.1 - - + -
54B ALA* 5.5 3.8 - - + -
72B PHE* 4.3 3.4 - + - -
102B ILE* 3.9 18.4 - - + -
103B CYS 3.8 2.2 - - - -
104B VAL* 4.1 16.2 - - + -
127B GLU* 3.8 46.4 - - + -
128B VAL* 3.9 22.2 - - + -
131B LEU* 3.9 28.3 - - + -
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Residues in contact with LEU 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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441A ASP* 4.8 8.3 - - - +
37B ARG* 3.4 44.6 - - + +
38B PHE* 1.3 75.1 - - - +
40B LEU* 1.3 62.3 + - - +
41B TYR* 3.6 11.2 - - + +
49B PHE* 3.8 39.5 - - + -
50B GLN 3.7 4.3 - - - -
51B GLU* 4.3 3.6 - - - +
102B ILE* 3.5 2.9 - - - +
103B CYS* 2.9 51.2 + - + +
105B ASP* 4.3 24.0 - - + +
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Residues in contact with LEU 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 PHE 3.7 1.8 + - - -
39B LEU* 1.3 72.0 - - - +
41B TYR* 1.3 62.7 + - - +
42B THR* 3.9 21.3 - - + -
45B ASN* 3.0 8.9 + - - +
49B PHE* 3.2 1.9 - - - -
50B GLN* 2.7 57.9 + - - +
52B ILE* 4.3 16.6 - - + -
62B SER* 3.6 15.0 - - - +
63B ASN 4.1 2.7 - - - +
64B PHE* 3.6 32.8 - - + +
100B ASN* 3.9 16.8 - - + +
101B CYS 3.7 2.0 - - - +
102B ILE* 3.7 26.5 - - + +
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Residues in contact with TYR 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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441A ASP* 3.8 12.6 + - - -
39B LEU* 3.6 20.0 - - + +
40B LEU* 1.3 76.1 - - - +
42B THR* 1.3 63.1 + - - +
45B ASN 3.6 5.6 - - - +
46B PRO 3.6 19.1 - - - -
47B ASP 3.9 14.8 - - - -
48B ASN* 4.0 3.8 - - - -
49B PHE* 3.6 43.6 - - + -
87B SER* 3.6 25.6 - - - -
90B CYS* 4.2 9.4 - - + -
91B GLN* 4.7 0.9 - - - -
94B PHE* 3.6 16.8 - - + -
101B CYS* 2.9 36.5 + - - +
103B CYS* 3.7 28.5 - - + -
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Residues in contact with THR 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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40B LEU* 3.9 22.0 - - + -
41B TYR* 1.3 77.9 - - - +
43B ASN* 1.3 64.3 + - - +
44B GLU* 3.0 18.5 + - - +
45B ASN* 2.7 44.8 + - - +
46B PRO* 3.1 5.5 - - - +
63B ASN* 3.8 14.0 - - + +
68B ARG* 3.5 26.7 - - - +
94B PHE* 3.5 8.5 - - - -
99B VAL 3.7 8.3 - - - +
100B ASN* 3.9 5.6 - - - +
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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