Contacts of the strand formed by residues 46 - 50 (chain B) in PDB entry 2ZJP
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 ALA 46 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37B LYS* 2.9 31.6 + - + +
44B TYR* 3.5 24.2 - - + -
45B GLU* 1.3 78.3 - - - +
47B VAL* 1.3 70.2 + - - +
80B GLU* 3.6 14.8 - - + +
81B PHE 3.0 16.6 - - - +
82B ARG* 3.9 8.7 - - + +
83B GLY 4.7 2.0 - - - +
84B PHE 5.5 1.3 - - - +
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Residues in contact with VAL 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ILE* 4.2 17.3 - - + -
35B GLN 4.1 2.5 - - - +
36B ARG* 4.7 21.5 - - + +
37B LYS* 5.3 0.2 - - - -
46B ALA* 1.3 80.8 - - - +
48B GLN* 1.3 75.7 + - - +
49B ILE* 3.4 7.4 + - + +
79B ARG 3.2 0.9 - - - +
80B GLU* 2.9 26.0 - - - -
81B PHE* 2.7 22.6 + - + +
84B PHE* 3.9 48.9 - - + +
85B ALA* 4.5 1.8 - - - +
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Residues in contact with GLN 48 (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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33B ILE* 3.3 7.4 - - - -
34B VAL* 2.9 37.9 + - + +
35B GLN* 2.7 56.1 + - + +
37B LYS* 5.1 1.0 - - + +
47B VAL* 1.3 75.3 - - - +
49B ILE* 1.3 60.8 + - - +
66B HIS* 2.6 30.9 + - - -
78B LEU* 4.2 13.8 - - + +
79B ARG 3.2 7.9 - - - +
80B GLU* 4.2 6.6 - - + +
2614X A 3.2 41.5 + - - +
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Residues in contact with ILE 49 (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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3B GLY 5.0 2.0 - - - +
4B ILE* 4.5 6.1 - - + -
5B LEU* 3.5 16.7 - - + +
31B CYS* 3.0 41.1 - - + +
32B PRO 2.8 14.4 - - - +
33B ILE* 4.9 2.0 - - + -
47B VAL* 3.4 5.5 + - + +
48B GLN* 1.3 76.5 - - - +
50B GLY* 1.3 60.6 + - - +
77B ILE 3.5 1.0 - - - +
78B LEU* 3.1 7.1 - - - -
79B ARG 2.5 42.4 + - - +
81B PHE* 3.3 36.3 - - + -
84B PHE* 5.5 3.8 - - + -
90B SER* 3.6 22.4 - - - +
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Residues in contact with GLY 50 (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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5B LEU* 4.8 1.6 - - - -
31B CYS* 2.9 16.5 - - - +
32B PRO* 2.5 46.1 + - - +
49B ILE* 1.3 76.0 - - - +
51B TYR* 1.3 59.1 + - - -
75B THR* 4.1 4.0 - - - -
77B ILE 3.2 6.5 - - - -
78B LEU* 3.8 14.7 - - - +
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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