Contacts of the strand formed by residues 32 - 39 (chain A) in PDB entry 5OND
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 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A ALA* 4.1 10.1 - - - +
31A PRO* 1.3 82.6 - - - +
33A ILE* 1.3 63.0 + - - +
47A SER* 3.5 24.5 - - - +
48A GLU* 3.4 28.0 - - - +
49A PRO* 3.6 23.8 - - + -
50A LEU* 4.3 5.1 - - - +
32B MET* 3.5 40.0 - - + +
34B THR* 4.9 2.6 + - - -
47B SER* 4.5 4.7 + - - +
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Residues in contact with ILE 33 (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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32A MET* 1.3 77.9 - - - +
34A THR* 1.3 73.9 + - - +
35A LEU* 3.8 26.7 + - + -
46A VAL 3.6 1.2 - - - +
47A SER* 3.5 2.5 - - - -
48A GLU* 2.9 38.9 + - + +
50A LEU* 3.7 28.3 - - + -
130A PHE* 3.7 37.5 - - + +
138A ARG* 3.9 21.1 - - - +
97B SER 5.8 0.4 - - - +
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Residues in contact with THR 34 (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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33A ILE* 1.3 79.2 - - - +
35A LEU* 1.3 64.0 + - - +
45A ALA* 4.4 5.2 - - + -
46A VAL 3.2 9.9 - - - +
47A SER* 4.0 7.7 + - - +
29B LEU* 4.1 19.5 - - + -
31B PRO* 3.5 26.4 - - + +
32B MET 4.9 2.4 + - - -
96B LEU* 4.0 25.2 - - + +
97B SER* 3.2 38.0 - - - +
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Residues in contact with LEU 35 (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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33A ILE* 3.8 30.1 - - + +
34A THR* 1.3 77.1 - - - +
36A GLU* 1.3 66.7 + - - +
37A LYS* 3.6 27.8 - - + +
45A ALA* 3.4 2.3 - - - -
46A VAL* 2.9 40.0 + - + +
48A GLU* 3.6 18.2 - - + +
130A PHE 5.4 1.8 - - - +
132A GLU 4.5 1.3 - - - +
133A PRO* 4.3 11.9 - - + -
138A ARG* 3.6 26.7 - - - +
97B SER* 3.8 10.3 - - - +
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Residues in contact with GLU 36 (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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35A LEU* 1.3 76.8 - - - +
37A LYS* 1.3 66.3 + - - +
43A ARG* 4.4 35.1 + - + +
44A THR 3.1 14.8 - - - +
45A ALA* 4.7 5.8 - - + -
133A PRO* 5.3 4.5 - - - +
93B ILE* 6.2 0.4 - - + +
94B HIS* 2.7 40.4 + - - -
97B SER* 3.2 17.1 + - - +
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Residues in contact with LYS 37 (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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35A LEU* 3.6 19.5 + - + +
36A GLU* 1.3 73.7 - - - +
38A ILE* 1.4 69.9 + - - +
39A VAL* 5.2 0.9 - - + -
43A ARG* 3.6 2.3 - - - +
44A THR* 2.8 35.7 + - - +
46A VAL* 3.8 21.5 - - + -
48A GLU* 2.8 31.4 + - - +
133A PRO* 2.7 45.0 + - - -
134A ASP* 4.8 2.1 - - - +
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Residues in contact with ILE 38 (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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37A LYS* 1.4 78.2 - - - +
39A VAL* 1.3 68.1 + - - +
41A GLY* 3.5 34.1 - - - +
42A LYS 3.4 1.6 - - - -
43A ARG* 3.7 54.5 - - + +
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Residues in contact with VAL 39 (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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37A LYS* 3.9 2.4 + - + +
38A ILE* 1.3 77.9 - - - +
40A ARG* 1.3 95.3 + - + +
41A GLY 3.2 0.4 - - - -
42A LYS* 2.9 23.5 + - - +
44A THR* 3.7 21.9 - - + +
46A VAL* 4.3 17.3 - - + -
27B ASN* 3.3 24.1 + - - +
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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