Contacts of the strand formed by residues 154 - 159 (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 PHE 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A TRP* 3.6 27.6 - + + +
39A TRP* 3.4 48.5 - + - -
85A ILE* 4.5 8.3 - - + -
87A ILE* 4.4 5.6 - - + -
141A PHE* 3.6 31.4 - + + -
142A SER 3.9 0.7 - - - +
143A ASP* 3.8 16.6 - - + +
151A SER* 4.2 1.3 - - - -
153A HIS* 1.3 80.5 - - - +
155A HIS* 1.3 76.1 + - - +
156A ILE* 3.7 12.1 - - + -
175A THR* 3.3 4.5 - - - +
176A TYR* 2.8 65.8 + + + -
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Residues in contact with HIS 155 (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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78A TYR* 4.7 0.9 - + - -
140A GLN 3.8 0.2 - - - +
141A PHE* 3.4 4.0 - - - -
142A SER* 2.9 58.5 + - - +
143A ASP* 5.2 0.9 - - - -
144A HIS* 4.0 14.7 + + - -
153A HIS* 6.1 1.8 + - - -
154A PHE* 1.3 78.6 - - - +
156A ILE* 1.3 61.4 + - - +
157A PHE* 4.3 4.3 - - + -
173A TRP* 3.8 27.3 + + + -
174A PRO 3.5 4.0 - - - +
175A THR* 2.5 39.4 + - + -
1196A SO4 4.6 13.2 + - - -
1199A SO4 3.3 37.9 + - - -
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Residues in contact with ILE 156 (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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85A ILE* 4.1 19.5 - - + -
92A ILE* 5.3 2.7 - - + -
94A PHE* 4.4 6.3 - - + -
139A VAL* 3.6 33.7 - - + -
140A GLN 3.2 9.4 - - - +
141A PHE* 3.9 19.7 - - + -
154A PHE* 3.7 8.1 - - + -
155A HIS* 1.3 75.1 - - - +
157A PHE* 1.3 65.6 + - - +
158A MET* 3.9 21.0 + - + +
173A TRP* 5.2 0.4 - - - -
174A PRO* 3.1 26.4 + - - +
176A TYR* 3.5 34.1 - - + -
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Residues in contact with PHE 157 (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* 3.4 50.7 - - - -
139A VAL* 3.2 7.3 - - - -
140A GLN* 2.8 49.5 + - + +
142A SER* 3.9 20.4 - - - -
155A HIS* 4.4 8.1 - - + -
156A ILE* 1.3 74.4 - - - +
158A MET* 1.3 60.3 + - - +
166A LEU* 3.3 21.1 - - + +
169A GLU* 3.6 20.0 - - + -
172A ASN 3.4 26.2 - - - -
173A TRP* 3.7 22.0 - + + -
174A PRO* 5.3 1.3 - - - -
1196A SO4 3.8 13.5 - - - -
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Residues in contact with MET 158 (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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80A THR* 4.4 1.8 - - - +
82A VAL* 4.3 16.2 - - + -
85A ILE* 4.7 1.8 - - - -
94A PHE* 3.6 29.8 - - - -
136A PRO* 3.8 21.8 - - + -
138A TYR 3.4 3.6 - - - -
139A VAL* 4.0 9.2 - - + -
156A ILE* 3.9 22.3 + - + +
157A PHE* 1.3 77.7 - - - +
159A GLY* 1.3 57.3 + - - +
166A LEU* 3.7 10.5 - - - +
174A PRO* 4.1 27.3 - - + +
176A TYR* 4.5 3.8 - - - +
1194A SO4 4.2 15.5 - - - +
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Residues in contact with GLY 159 (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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136A PRO* 4.1 2.7 - - - +
137A LYS 3.3 4.7 + - - -
138A TYR* 2.9 38.1 + - - -
158A MET* 1.3 74.3 - - - +
160A ASN* 1.3 66.6 + - - -
161A THR 3.7 2.7 - - - -
162A SER 5.5 0.2 - - - -
166A LEU* 3.7 17.5 - - - +
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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