Contacts of the strand formed by residues 17 - 28 (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 LEU 17 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B LEU* 3.8 24.2 - - + +
16B THR* 1.3 88.5 - - + +
18B VAL* 1.3 61.3 + - - +
19B ILE* 4.1 9.6 - - - +
20B GLN* 3.8 32.8 - - + +
41B LEU* 3.8 32.3 - - + -
42B LEU 3.5 17.5 - - - +
43B SER* 4.2 4.7 - - - +
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Residues in contact with VAL 18 (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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16B THR* 3.8 4.0 - - + +
17B LEU* 1.3 78.5 - - - +
19B ILE* 1.3 63.5 + - - +
42B LEU* 2.9 25.7 + - + +
43B SER 3.7 24.2 - - - +
44B THR* 3.9 2.2 - - + +
121B ARG* 4.2 27.7 + - + +
125B GLU* 3.7 18.6 - - - +
130B ARG* 3.7 23.6 - - - +
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Residues in contact with ILE 19 (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* 3.8 5.7 - - - +
18B VAL* 1.3 81.0 - - - +
20B GLN* 1.3 71.6 + - - +
21B GLN* 5.9 0.9 - - + -
40B LEU 4.1 0.2 - - - +
41B LEU* 3.7 0.5 - - - -
42B LEU* 2.9 43.8 + - + +
114B GLY 5.3 1.3 - - - +
117B GLU* 3.7 37.0 - - + +
118B PHE* 3.8 31.5 - - + +
121B ARG* 3.7 32.3 - - + +
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Residues in contact with GLN 20 (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* 3.8 22.8 - - + +
19B ILE* 1.3 83.4 - - - +
21B GLN* 1.3 66.8 + - - +
39B THR* 4.4 10.9 - - + +
40B LEU 3.2 9.0 - - - +
41B LEU* 4.0 23.2 - - + +
118B PHE* 4.6 0.7 - - - -
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Residues in contact with GLN 21 (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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19B ILE* 5.5 1.1 - - + +
20B GLN* 1.3 79.4 - - - +
22B ARG* 1.3 85.3 + - - +
24B VAL* 3.6 17.9 - - + +
39B THR* 4.2 4.4 - - - +
40B LEU 2.7 38.5 + - - +
110B PHE* 3.8 7.2 - - + -
112B GLU* 3.5 17.4 + - - +
113B HIS 2.8 29.0 + - - +
114B GLY* 3.9 12.7 - - - +
118B PHE* 4.1 18.4 - - + -
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Residues in contact with ARG 22 (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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21B GLN* 1.3 103.9 + - - +
23B GLY* 1.3 63.7 + - - +
39B THR* 3.8 21.5 + - + +
52B GLN* 4.7 12.6 + - - +
110B PHE* 6.0 0.2 - - - -
112B GLU* 3.5 23.4 + - - +
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Residues in contact with GLY 23 (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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22B ARG* 1.3 75.4 - - - +
24B VAL* 1.3 62.6 + - - +
25B ARG* 5.1 1.1 - - - +
37B ALA* 6.2 0.4 - - - -
38B GLY 3.2 11.8 + - - -
52B GLN* 4.1 6.2 - - - +
111B LYS* 3.0 37.2 + - - +
112B GLU* 3.6 26.0 + - - -
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Residues in contact with VAL 24 (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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21B GLN* 3.6 26.2 - - + +
22B ARG 3.8 0.9 - - - +
23B GLY* 1.3 78.6 - - - +
25B ARG* 1.3 71.2 + - - +
26B ILE* 4.8 2.2 - - + -
38B GLY 2.7 32.9 + - - +
40B LEU* 3.8 30.5 - - + -
49B TRP* 2.9 14.5 - - + -
108B LEU* 4.3 11.0 - - + -
109B SER 3.2 10.3 - - - +
110B PHE* 3.6 32.5 - - + -
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Residues in contact with ARG 25 (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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23B GLY 4.0 1.5 + - - +
24B VAL* 1.3 76.9 - - - +
26B ILE* 1.3 62.3 + - - +
27B TYR* 3.3 32.2 + - + -
35B PHE* 4.2 18.6 - - - +
36B ASP 3.2 20.4 - - - +
37B ALA* 4.0 13.4 - - + +
49B TRP* 4.1 0.2 - - - -
107B LYS 3.4 2.3 - - - +
108B LEU* 3.5 3.3 - - - -
109B SER* 2.9 47.5 + - - +
111B LYS* 3.4 48.1 - - + +
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Residues in contact with ILE 26 (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* 4.3 20.0 - - + -
24B VAL* 4.8 1.8 - - + -
25B ARG* 1.3 75.5 - - - +
27B TYR* 1.3 70.0 + - - +
35B PHE 3.1 19.9 + - - -
36B ASP* 3.2 18.1 + - + +
40B LEU* 4.6 5.6 - - + -
47B LEU* 6.4 0.4 - - + -
49B TRP* 3.3 48.9 - - + -
106B ILE* 4.4 20.4 - - + -
107B LYS 3.4 4.5 - - - +
108B LEU* 3.7 20.4 - - + -
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Residues in contact with TYR 27 (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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25B ARG* 3.3 36.3 + - + -
26B ILE* 1.3 79.7 - - - +
28B ASP* 1.3 60.7 + - - +
29B GLY 5.2 1.3 - - - +
31B GLU* 3.7 9.2 - - + -
32B LYS* 3.4 40.8 - - + +
33B ILE* 3.9 14.0 - - - +
34B LYS 4.3 9.2 - - - -
35B PHE* 4.1 10.9 - + + +
81B LYS* 4.8 14.6 - - - -
106B ILE* 3.6 8.5 - - - +
107B LYS* 3.0 48.7 + - + +
109B SER* 3.7 28.7 - - - -
111B LYS* 5.0 2.9 + - - -
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Residues in contact with ASP 28 (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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26B ILE 4.2 0.2 + - - -
27B TYR* 1.3 73.2 - - - +
29B GLY* 1.3 67.2 + - - +
30B GLU 3.0 4.2 + - - -
31B GLU* 3.2 23.5 + - + +
34B LYS 3.6 18.6 + - - +
35B PHE 4.5 0.2 - - - +
103B ASN* 5.0 8.3 - - - +
105B TYR 4.4 5.7 - - - +
106B ILE* 4.7 9.2 - - + +
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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