Contacts of the strand formed by residues 136 - 141 (chain A) in PDB entry 4ZCH
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 136 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A HIS* 3.6 20.0 - + + +
12A LEU 3.3 15.7 - - - +
13A VAL* 4.5 0.2 - - + -
30A TRP* 3.7 10.0 - - - -
58A TYR* 3.6 26.9 - + - -
59A SER* 3.6 3.1 + - - -
60A GLN* 2.9 59.7 + - + +
104A TYR* 4.3 2.5 - + - -
132A PRO 3.6 18.6 - - - +
133A HIS* 3.4 21.5 - - - -
135A THR* 1.3 77.0 - - - +
137A LEU* 1.3 61.2 + - - +
389A PHE* 3.9 15.5 - + - -
406A SER* 3.8 13.0 - - - -
407A ALA 3.2 28.3 - - - -
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Residues in contact with LEU 137 (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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11A HIS* 3.5 1.7 + - - -
12A LEU* 2.7 41.2 + - + +
30A TRP* 3.6 46.9 - - + +
47A VAL* 4.0 20.0 - - + -
57A LEU* 3.8 21.3 - - + -
58A TYR* 3.5 19.5 - - - +
59A SER* 4.2 6.7 - - - -
74A VAL* 5.0 2.5 - - + -
117A LEU* 5.3 4.7 - - + +
118A SER 5.5 0.9 - - - -
119A VAL* 3.8 24.7 - - + +
136A PHE* 1.3 74.8 - - - +
138A GLY* 1.3 59.9 + - - +
139A PHE* 3.8 11.7 - - + -
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Residues in contact with GLY 138 (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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10A LEU 3.1 10.1 - - - -
57A LEU* 3.3 12.0 - - - +
58A TYR* 2.9 59.1 + - - -
137A LEU* 1.3 76.4 - - - +
139A PHE* 1.3 64.0 + - - -
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Residues in contact with PHE 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A SER 4.7 0.2 - - - -
9A VAL* 3.4 5.9 - - - -
10A LEU* 2.9 36.6 + - + +
12A LEU* 3.7 25.4 - - + -
40A LEU* 3.8 35.0 - - + -
47A VAL* 3.8 24.2 - - + -
49A ILE* 4.4 3.1 - - + -
55A TYR* 4.2 7.2 - + + -
56A LEU 3.3 7.6 - - - -
57A LEU* 3.6 19.5 - - + -
58A TYR* 4.0 2.2 - - - -
111A LEU* 4.6 11.0 - - + -
117A LEU* 3.5 34.3 - - + -
137A LEU* 3.8 17.3 - - + -
138A GLY* 1.3 77.2 - - - -
140A VAL* 1.3 62.7 + - - +
141A LYS 4.3 0.4 - - - -
409A ILE* 3.6 3.8 - - - +
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Residues in contact with VAL 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A SER 3.9 2.5 - - - -
9A VAL* 4.8 7.0 - - + +
55A TYR* 3.2 4.2 - - - -
56A LEU* 2.8 60.4 + - + +
58A TYR* 4.8 4.3 - - + -
139A PHE* 1.3 71.2 - - - +
141A LYS* 1.4 73.3 + - - +
142A LEU* 3.6 9.2 + - + +
353A PHE* 4.9 2.2 - - + -
409A ILE* 3.5 32.8 - - + -
443A LEU* 4.0 34.8 - - + -
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Residues in contact with LYS 141 (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 HIS* 3.9 33.3 + - + +
8A SER 3.1 25.1 + - - +
51A ASP* 2.8 39.9 + - - +
52A ALA 2.9 20.2 + - - -
53A GLY* 4.0 5.5 - - - -
54A VAL 3.5 12.1 - - - +
55A TYR* 3.5 25.1 - - + +
140A VAL* 1.4 81.0 - - - +
142A LEU* 1.3 69.9 + - - +
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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