Contacts of the strand formed by residues 21 - 27 (chain A) in PDB entry 2H18
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 MET 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A PHE* 3.8 30.7 - - + +
19A GLU* 3.3 35.3 + - + +
20A GLU* 1.3 75.3 - - - +
22A GLU* 1.3 63.6 + - - +
23A LEU* 4.2 11.7 - - + -
64A ASN 3.3 5.1 + - - +
65A VAL* 3.4 8.3 - - + +
66A THR* 2.9 26.8 + - - +
90A SER* 3.9 13.5 - - - -
91A ALA* 6.1 1.6 - - - -
177A LEU* 3.6 32.1 - - - +
180A HIS 4.8 0.7 - - - -
181A SER* 3.7 28.5 - - - +
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Residues in contact with GLU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A MET* 1.3 74.4 - - - +
23A LEU* 1.3 60.4 + - - +
66A THR* 3.4 24.1 - - + +
68A LYS* 2.8 36.8 + - + -
87A ARG 3.7 14.6 - - - +
88A GLY* 4.5 6.6 - - - +
89A VAL* 3.6 24.0 - - + +
90A SER* 2.7 38.6 + - - +
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Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A PHE* 4.1 9.9 - - + -
21A MET* 4.2 15.7 - - - +
22A GLU* 1.3 76.6 - - - +
24A THR* 1.3 63.8 + - - +
25A LEU* 5.3 1.6 - - + -
36A PHE* 6.0 2.9 - - + -
40A ILE* 6.2 0.2 - - + -
65A VAL* 3.7 30.3 - - + -
66A THR 3.0 9.0 + - - +
67A ILE* 3.4 27.8 - - + -
68A LYS* 2.8 27.0 + - - +
89A VAL* 3.8 7.2 - - - +
91A ALA* 3.5 20.4 - - + +
93A VAL* 3.8 26.5 - - + -
177A LEU* 4.1 16.8 - - + -
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Residues in contact with THR 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 1.3 76.7 - - - +
25A LEU* 1.3 59.1 + - - +
26A VAL* 4.2 6.1 - - + -
67A ILE* 4.7 0.4 - - - -
68A LYS* 2.7 22.4 + - - -
70A TRP* 2.8 22.3 + - - -
86A CYS* 3.5 25.8 - - + -
89A VAL* 3.9 6.5 - - + +
91A ALA 3.2 5.1 + - - +
92A ILE* 3.6 37.2 - - + -
93A VAL* 2.8 31.1 + - - +
114A LEU* 5.7 1.3 - - + -
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Residues in contact with LEU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 5.3 2.7 - - + -
24A THR* 1.3 72.8 - - - +
26A VAL* 1.3 61.6 + - - +
33A LYS* 3.7 27.6 - - + +
36A PHE* 4.0 14.8 - - + -
37A VAL* 3.5 31.6 - - + -
67A ILE* 3.6 19.4 - - + +
68A LYS 2.9 7.2 + - - +
69A LEU* 3.2 19.2 - - + +
70A TRP 3.2 22.5 + - - -
93A VAL* 3.4 35.0 - - + +
95A MET* 4.2 15.7 - - + -
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Residues in contact with VAL 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A THR* 4.2 9.4 - - + -
25A LEU* 1.3 77.3 - - - +
27A GLY* 1.3 62.1 + - - +
33A LYS* 3.4 6.2 - - - +
70A TRP* 3.3 49.4 - - + +
72A ILE* 3.6 23.1 - - + -
92A ILE* 4.1 10.3 - - + -
93A VAL 3.1 8.9 + - - +
94A TYR* 3.2 16.4 - - + -
95A MET 3.0 22.2 + - - -
114A LEU* 4.0 22.7 - - + -
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Residues in contact with GLY 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A VAL* 1.3 81.1 - - - +
28A LEU* 1.3 68.7 + - - -
33A LYS* 3.1 14.4 + - - +
71A ASP* 3.5 0.7 - - - -
72A ILE* 3.0 30.1 + - - -
94A TYR* 4.0 9.6 - - - -
95A MET 3.6 15.0 - - - -
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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