Contacts of the strand formed by residues 38 - 43 (chain B) in PDB entry 2HTH
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 GLY 38 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B GLY* 3.2 4.6 + - - -
24B VAL* 2.7 45.7 + - - +
37B ALA* 1.3 75.1 - - - +
39B THR* 1.3 63.3 + - - -
40B LEU 3.6 0.2 + - - -
49B TRP* 2.9 11.2 - - - -
50B ARG 3.8 5.4 - - - -
52B GLN* 3.4 20.8 - - - +
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Residues in contact with THR 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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20B GLN* 4.4 14.4 - - - +
21B GLN 3.4 16.4 - - - +
22B ARG* 3.8 21.4 - - + +
38B GLY* 1.3 72.3 - - - -
40B LEU* 1.3 63.5 + - - +
41B LEU* 3.9 19.7 - - + +
48B ILE 3.8 1.0 - - - +
49B TRP* 3.6 5.6 - - - -
50B ARG* 3.0 47.3 + - - +
52B GLN* 3.7 8.1 + - - +
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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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4B PHE* 6.1 0.9 - - + -
20B GLN* 3.2 3.6 - - - +
21B GLN 2.7 41.9 + - - +
24B VAL* 3.8 27.6 - - + -
26B ILE* 4.6 7.9 - - + -
38B GLY 3.6 1.6 + - - -
39B THR* 1.3 72.5 - - - +
41B LEU* 1.3 62.0 + - - +
47B LEU* 4.1 21.8 - - + -
48B ILE 3.7 17.3 - - - +
49B TRP* 4.5 16.2 - - + -
108B LEU* 3.6 30.3 - - + -
110B PHE* 4.5 4.3 - - + -
118B PHE* 3.6 29.9 - - + -
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Residues in contact with LEU 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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11B LEU* 6.1 2.5 - - + -
17B LEU* 3.8 27.4 - - + -
19B ILE 3.7 3.6 - - - -
20B GLN* 4.0 23.1 - - + +
39B THR* 3.9 22.2 - - + +
40B LEU* 1.3 76.3 - - - +
42B LEU* 1.3 59.1 + - - +
43B SER 4.0 0.2 - - - -
46B ARG 3.9 0.5 - - - +
47B LEU* 3.4 6.2 - - - +
48B ILE* 2.8 73.2 + - + +
50B ARG* 4.4 21.1 - - + +
118B PHE* 4.4 3.6 - - - -
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Residues in contact with LEU 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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17B LEU* 3.5 4.8 - - - +
18B VAL* 2.9 27.3 + - + -
19B ILE* 2.9 27.9 + - + +
41B LEU* 1.3 73.2 - - - +
43B SER* 1.3 77.4 + - - +
46B ARG 3.7 1.3 - - - +
47B LEU* 3.8 11.4 - - + -
63B LEU* 3.8 29.2 - - + -
118B PHE* 3.9 12.0 - - + -
121B ARG* 3.7 21.8 - - + +
122B LEU* 3.6 35.7 - - + +
125B GLU* 3.8 10.1 - - + -
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Residues in contact with SER 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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11B LEU* 4.7 9.2 - - - -
15B GLU* 2.8 33.8 + - - -
16B THR 3.0 18.4 - - - -
17B LEU* 4.2 4.3 - - - +
18B VAL* 3.7 7.4 - - - +
41B LEU 4.0 0.2 - - - -
42B LEU* 1.3 91.6 - - - +
44B THR* 1.3 63.7 + - - +
45B HIS 3.2 1.0 + - - -
46B ARG* 2.8 25.1 + - - +
48B ILE* 4.4 4.4 - - - +
63B LEU* 3.6 5.4 - - - +
125B GLU* 4.1 1.7 - - - +
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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