Contacts of the strand formed by residues 53 - 58 (chain A) in PDB entry 4Z8J
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 PHE 53 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ILE* 4.5 4.7 - - + -
51A TYR* 3.6 28.3 - - + -
52A GLY* 1.3 79.4 - - - +
54A ASN* 1.3 76.9 + - - +
55A VAL* 4.3 8.1 - - + -
79A VAL* 4.2 24.9 - - + -
81A ALA 3.2 14.8 - - - +
82A VAL* 4.4 1.8 - - + +
83A LEU 4.7 0.2 - - - +
88A ALA* 3.9 20.4 - - + -
93A VAL* 5.0 1.8 - - + -
99A ILE* 4.8 2.7 - - + -
119A ILE* 4.0 22.7 - - + -
126A LEU* 3.6 26.0 - - + -
128A LEU* 4.3 10.8 - - + -
592B VAL* 4.7 1.0 - - - +
593B MET* 2.8 48.8 + - + +
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Residues in contact with ASN 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A PHE* 1.3 85.6 - - - +
55A VAL* 1.3 60.1 + - - +
79A VAL* 3.3 7.3 - - - +
80A SER* 3.0 36.0 + - - +
81A ALA* 2.9 26.6 + - + +
590B GLU* 2.9 22.3 + - + +
591B THR 3.2 7.9 - - - +
592B VAL* 3.7 35.0 - - - +
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Residues in contact with VAL 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A PHE* 4.3 11.6 - - + -
54A ASN* 1.3 74.9 - - - +
56A ARG* 1.3 63.8 + - - +
77A GLN* 3.9 16.8 - - + -
78A HIS 3.3 10.5 - - - +
80A SER* 3.9 0.9 - - - -
99A ILE* 3.8 20.9 - - + -
112A HIS* 3.2 17.0 - - + -
115A VAL* 4.2 9.0 - - + -
116A VAL* 4.1 10.1 - - + -
119A ILE* 4.2 6.1 - - + -
590B GLU* 3.2 2.8 - - - +
591B THR* 2.9 34.6 + - - +
593B MET* 3.8 26.7 - - + -
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Residues in contact with ARG 56 (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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55A VAL* 1.3 76.4 - - - +
57A GLY* 1.3 60.1 + - - +
77A GLN* 3.5 5.9 - - - -
78A HIS* 2.8 48.7 + - + -
80A SER* 3.6 23.8 - - - +
588B GLU* 3.3 37.9 + - - +
589B TRP 3.2 10.5 - - - +
590B GLU* 2.9 37.3 + - + +
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Residues in contact with GLY 57 (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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56A ARG* 1.3 77.4 - - - +
58A GLN* 1.3 63.6 + - - -
76A LEU 5.2 1.8 - - - -
77A GLN* 3.0 19.5 + - - +
78A HIS* 5.0 1.8 - - - -
112A HIS* 3.9 2.3 + - - +
588B GLU* 3.2 17.9 - - - -
589B TRP 2.9 31.4 + - - +
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Residues in contact with GLN 58 (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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57A GLY* 1.3 73.6 - - - -
59A VAL* 1.3 59.2 + - - +
60A SER* 2.8 32.0 + - - +
62A GLY 2.7 35.9 + - - +
63A GLY* 5.1 0.9 - - - -
75A PRO* 3.3 27.0 + - + +
76A LEU 5.8 1.7 + - - -
77A GLN* 3.0 16.2 + - - +
109A GLY 3.7 8.1 + - - -
110A ALA 4.0 2.2 + - - -
112A HIS* 3.0 24.4 + - - +
587B GLU 3.3 12.6 - - - +
588B GLU* 4.1 7.3 + - + +
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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