Contacts of the strand formed by residues 50 - 54 (chain A) in PDB entry 2ZGH
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 50 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 4.3 12.3 - - + -
19A GLN 3.2 16.8 - - - +
20A ARG* 4.0 8.1 - - + -
25A LEU* 3.7 29.6 - - + -
42A CYS 4.9 1.1 - - - +
43A LEU* 3.9 28.0 - - + -
45A GLN* 4.1 20.2 - - + +
46A ARG 4.0 9.2 - - - +
47A MET* 2.9 26.6 + - + +
49A GLN* 1.3 79.0 - - - +
51A ARG* 1.3 76.1 + - - +
67A HIS* 4.8 0.3 - - - -
68A ILE* 3.7 28.3 + - + +
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Residues in contact with ARG 51 (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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17A SER 3.7 0.3 - - - +
18A LEU* 3.6 5.7 - - - +
19A GLN* 2.8 39.2 + - + +
21A ASN 6.0 1.6 - - - +
22A GLY 6.0 2.7 - - - +
47A MET 4.8 0.2 + - - -
48A ALA 3.2 26.1 + - - -
49A GLN* 3.9 10.5 - - - +
50A LEU* 1.3 86.4 + - - +
52A LEU* 1.3 63.7 + - - +
53A VAL* 4.2 5.2 - - + -
65A THR* 3.7 21.3 - - + -
66A PHE 3.5 9.0 - - - +
67A HIS* 3.4 40.6 + - - -
68A ILE* 4.4 3.6 - - - -
243A SO4 3.2 35.8 + - - +
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Residues in contact with LEU 52 (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 ALA* 4.1 11.9 - - + -
17A SER 3.6 0.4 - - - -
18A LEU* 3.8 35.2 - - + +
28A GLY* 5.7 0.4 - - - -
36A VAL* 3.9 28.0 - - + -
38A THR* 6.2 0.4 - - - -
51A ARG* 1.3 72.8 - - - +
53A VAL* 1.3 60.9 + - - +
54A LEU* 4.2 3.8 - - + -
64A LEU 3.7 1.7 - - - +
65A THR* 3.5 2.3 - - - +
66A PHE* 2.8 40.2 + - + +
68A ILE* 4.0 11.6 - - + +
90A LEU* 3.7 33.0 - - + -
92A LEU* 3.5 33.2 - - + -
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Residues in contact with VAL 53 (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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15A MET 4.2 0.7 - - - +
16A ALA* 3.6 3.6 - - - -
17A SER* 3.0 34.7 + - - +
19A GLN* 3.7 28.3 - - + +
51A ARG* 4.8 3.6 - - + -
52A LEU* 1.3 77.9 - - - +
54A LEU* 1.3 66.0 + - - +
56A LEU* 3.7 31.8 - - + +
61A SER 5.2 0.2 - - - +
62A PRO 3.3 25.4 - - - +
64A LEU 3.4 11.2 - - - +
65A THR* 3.8 20.4 - - + +
125A TRP* 5.5 0.3 - - - -
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Residues in contact with LEU 54 (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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15A MET 4.1 6.5 - - - +
16A ALA* 3.7 30.7 - - + -
30A LEU* 4.1 14.6 - - + -
36A VAL* 4.3 12.3 - - + -
52A LEU* 4.9 3.4 - - + +
53A VAL* 1.3 76.6 - - - +
55A GLY* 1.3 64.4 + - - +
56A LEU 3.2 4.0 + - - -
63A GLY* 3.4 3.5 - - - -
64A LEU* 2.8 33.9 + - - +
66A PHE* 3.4 33.7 - - + -
92A LEU* 4.5 2.5 - - + -
96A VAL* 3.4 23.1 - - + -
102A ILE* 3.8 28.0 - - + +
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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