Contacts of the strand formed by residues 138 - 142 (chain A) in PDB entry 4ARH
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 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A TYR* 5.1 0.2 - - - -
126A PHE 3.6 2.0 - - - -
127A GLU* 3.9 29.3 + - + -
136A PRO* 3.8 1.7 - - - +
137A LYS* 1.3 97.3 - - + +
139A VAL* 1.3 70.3 + - - +
158A MET* 3.4 1.6 - - - -
159A GLY 2.9 38.4 + - - +
160A ASN 3.6 10.0 + - - -
161A THR 3.5 14.5 + - - -
162A SER* 3.5 37.0 - - - +
163A GLN* 3.7 38.8 - - + +
166A LEU* 4.0 11.7 - - + -
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Residues in contact with VAL 139 (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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92A ILE* 4.3 7.4 - - + -
94A PHE* 4.1 9.2 - - + -
105A TYR* 4.0 19.5 - - + -
125A LEU* 3.5 0.3 - - - -
126A PHE* 2.7 39.7 + - + +
136A PRO* 4.0 13.7 - - + -
138A TYR* 1.3 81.7 - - - +
140A GLN* 1.3 66.1 + - - +
141A PHE* 3.6 23.8 - - + -
156A ILE* 3.6 21.3 - - + -
157A PHE 3.2 3.8 - - - -
158A MET* 4.0 21.3 - - + -
163A GLN* 4.0 0.3 + - - -
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Residues in contact with GLN 140 (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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123A ARG* 2.9 45.0 + - + -
124A TYR 3.2 7.0 - - - +
125A LEU* 3.9 10.7 - - + +
139A VAL* 1.3 79.1 - - - +
141A PHE* 1.3 63.0 + - - +
156A ILE* 3.2 5.2 - - - +
157A PHE* 2.8 38.0 + - + +
163A GLN* 2.8 49.4 + - - +
166A LEU* 3.5 21.2 - - + +
167A LEU* 3.7 15.9 - - - +
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Residues in contact with PHE 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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32A LEU* 3.8 22.4 - - + -
35A TRP* 3.6 46.2 - + + +
87A ILE* 3.6 24.0 - - + -
92A ILE* 4.2 4.9 - - + -
122A VAL 3.8 0.7 - - - +
123A ARG* 3.2 6.3 - - - -
124A TYR* 2.8 35.7 + - - +
126A PHE* 3.7 23.8 - + - -
139A VAL* 3.6 17.9 - - + -
140A GLN* 1.3 73.7 - - - +
142A SER* 1.3 61.0 + - - +
143A ASP 4.3 0.2 - - - -
154A PHE* 3.6 38.6 - + + -
155A HIS 3.4 1.8 - - - -
156A ILE* 3.9 15.0 - - + -
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Residues in contact with SER 142 (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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115A TYR* 4.3 14.0 + - - -
121A GLY* 5.7 0.3 - - - -
122A VAL 3.7 16.8 + - - -
123A ARG* 4.5 8.1 + - - +
124A TYR* 5.7 0.2 - - - -
141A PHE* 1.3 76.6 - - - +
143A ASP* 1.3 61.3 + - - +
144A HIS* 3.9 2.6 + - - -
155A HIS* 2.9 44.2 + - - +
157A PHE* 3.9 25.5 - - - -
1196A SO4 5.1 2.8 + - - -
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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