Contacts of the strand formed by residues 135 - 139 (chain E) in PDB entry 4Z07
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 TYR 135 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A TYR* 3.5 20.8 + - - -
135A TYR* 3.6 54.5 + + + -
208A ASP* 4.3 4.7 + - - +
99E TYR* 3.5 34.1 - + + -
133E CYS 4.2 2.7 - - - -
134E MET* 1.3 74.1 - - - +
136E PRO* 1.3 82.5 - - + +
137E VAL* 3.9 8.2 - - + +
154E LEU* 3.7 28.9 - - + +
205E TRP* 3.4 5.9 - - - -
206E ALA* 2.7 60.0 + - + -
207E ILE* 4.9 0.2 - - - -
208E ASP* 4.5 13.0 - - + -
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Residues in contact with PRO 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A TYR* 3.3 22.3 + - + -
99E TYR* 4.8 8.1 - - + -
100E PRO 5.7 1.6 - - - +
135E TYR* 1.3 92.8 - - + +
137E VAL* 1.3 62.5 + - - +
138E GLU* 5.7 2.9 - - + -
203E LYS* 5.5 7.0 - - + -
204E LEU 3.6 8.1 - - - +
205E TRP* 3.6 27.4 - - + -
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Residues in contact with VAL 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A PRO* 3.9 15.9 - - + -
99A TYR* 3.4 24.7 - - + +
135E TYR* 3.9 6.1 - - + +
136E PRO* 1.3 78.3 - - - +
138E GLU* 1.3 67.2 + - - +
139E TYR* 3.5 28.9 - - + +
154E LEU* 5.7 1.8 - - + -
156E TYR* 4.8 5.2 - - + -
203E LYS* 3.6 2.9 - - - +
204E LEU* 2.7 48.4 + - + +
205E TRP 5.0 0.2 - - - -
206E ALA* 3.6 32.3 - - + +
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Residues in contact with GLU 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A PRO* 4.7 0.2 - - - +
98A PHE 4.6 19.2 + - - +
99A TYR* 5.4 2.2 - - - -
100A PRO* 6.1 0.5 - - - +
136E PRO* 5.7 2.7 - - + -
137E VAL* 1.3 84.6 - - - +
139E TYR* 1.3 73.2 + - - +
202E VAL 3.3 11.7 - - - +
203E LYS* 4.5 20.1 - - + +
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Residues in contact with TYR 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A THR* 3.4 26.0 + - + -
96A LEU 4.1 4.5 - - - -
97A PRO* 3.6 31.0 - - + +
137E VAL* 3.5 24.2 - - + +
138E GLU* 1.3 78.7 - - - +
140E GLY* 1.3 68.6 + - - +
143E SER* 4.2 15.9 - - - +
145E ILE* 3.9 34.8 + - + +
156E TYR* 4.1 10.9 + + - -
198E THR* 4.0 5.4 - - + -
201E ASN* 3.4 4.2 - - - +
202E VAL* 2.9 42.8 + - + +
204E LEU* 3.8 26.5 - - + -
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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