Contacts of the strand formed by residues 34 - 39 (chain A) in PDB entry 2M72
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 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A THR* 3.8 4.0 - - + +
6A TYR 3.1 33.9 - - - +
7A ALA* 4.2 8.3 - - + -
27A LEU* 4.1 9.2 - - + +
28A GLU 4.5 1.8 - - - -
29A ASN* 3.3 52.3 - - + +
32A LYS 3.8 4.7 - - - +
33A PRO* 1.3 79.6 - - - +
35A ILE* 1.3 62.8 + - - +
36A ILE 4.1 0.4 - - - -
66A VAL* 4.1 0.4 - - - -
67A ARG* 3.4 7.9 - - + +
69A ILE* 3.5 31.0 - - + -
94A GLU* 5.2 0.9 - - - +
117A ILE* 3.6 1.0 - - - +
118A VAL* 2.6 49.5 + - + +
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Residues in contact with ILE 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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34A MET* 1.3 75.4 - - - +
36A ILE* 1.3 63.3 + - - +
37A SER* 3.8 7.3 + - - +
49A GLU* 5.9 0.4 - - + +
53A ILE* 4.3 4.5 - - + -
60A TRP* 3.9 26.9 - - + -
66A VAL* 3.5 26.2 - - + -
67A ARG 2.9 8.3 + - - -
68A LEU* 3.4 26.7 - - + +
69A ILE* 2.7 31.6 + - - +
115A VAL* 3.9 26.7 - - + -
116A PHE 3.4 4.0 - - - +
117A ILE* 4.1 17.5 - - + -
139A LEU* 4.2 10.5 - - + -
143A VAL* 4.9 3.8 - - + -
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Residues in contact with ILE 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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7A ALA* 4.3 10.3 - - + -
9A LEU* 3.8 38.6 - - + -
27A LEU* 5.5 0.4 - - + -
35A ILE* 1.3 76.3 - - - +
37A SER* 1.3 61.4 + - - +
38A PHE* 3.5 27.2 - - + -
69A ILE* 3.3 31.2 - - + +
71A VAL* 3.5 21.8 - - + -
103A PHE* 4.7 5.8 - - + -
114A ALA 3.3 6.4 - - - +
115A VAL* 3.7 1.4 - - - -
116A PHE* 2.8 43.1 + - + +
118A VAL* 4.9 7.0 - - + -
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Residues in contact with SER 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 ILE* 3.8 12.7 + - - +
36A ILE* 1.3 72.1 - - - +
38A PHE* 1.3 62.0 + - - +
39A PHE* 3.6 9.2 - - - -
49A GLU* 2.7 27.9 + - - -
50A LEU* 3.8 25.4 - - - +
53A ILE* 5.4 1.0 - - - +
68A LEU* 5.1 3.3 - - - +
69A ILE 2.8 12.1 + - - -
70A ALA* 4.8 2.0 - - - -
71A VAL* 3.0 28.8 + - - +
114A ALA 3.6 4.3 - - - -
115A VAL* 5.2 1.2 - - - +
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Residues in contact with PHE 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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9A LEU* 5.9 0.4 - - + -
36A ILE* 3.5 21.8 - - + -
37A SER* 1.3 72.3 - - - +
39A PHE* 1.3 59.7 + - - +
71A VAL* 3.5 12.3 - - + -
73A ILE* 3.8 16.6 - - + -
103A PHE* 3.4 40.8 - + - -
104A LYS* 4.5 2.9 - - - -
107A MET* 3.6 24.0 - - + -
109A VAL* 3.6 22.9 - - + -
112A ILE* 3.5 8.8 - - - +
113A PRO* 3.8 5.5 - - - +
114A ALA* 3.0 49.9 + - + +
116A PHE* 3.2 29.6 - + + -
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Residues in contact with PHE 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 SER* 3.6 15.0 - - - -
38A PHE* 1.3 75.0 - - - +
40A ALA* 1.3 86.0 + - - +
43A CYS* 5.2 2.9 - - + -
47A LEU* 3.3 37.0 - - + -
50A LEU* 5.0 3.4 - - + -
70A ALA* 3.6 25.4 - - + -
71A VAL 3.3 22.4 + - - +
72A SER* 3.8 2.0 - - - -
73A ILE* 3.1 29.3 + - - +
82A VAL* 3.4 31.4 - - + -
85A LEU* 4.7 8.3 - - + -
91A TRP* 3.6 28.0 - + - -
112A ILE* 4.2 8.1 - - + -
113A PRO* 5.9 1.3 - - + -
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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