Contacts of the strand formed by residues 185 - 191 (chain A) in PDB entry 4F2N
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 ARG 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A TYR* 3.5 63.0 - - + +
160A CYS* 4.1 1.8 - - - -
161A VAL* 2.8 41.9 + - - +
163A PRO* 3.7 32.7 - - + +
183A GLY 4.6 1.1 - - - +
184A LEU* 1.3 76.3 - - - +
186A PRO* 1.3 69.2 - - - +
187A ILE* 3.7 2.4 + - - +
227A ARG 4.7 0.8 + - - -
228A ALA* 2.8 52.5 + - + -
230A LYS* 4.4 11.1 + - - -
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Residues in contact with PRO 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TYR* 5.1 0.3 + - - -
25A THR* 3.4 29.9 + - + +
106A PHE* 4.5 10.1 - - + -
110A PHE* 3.7 13.0 - - + -
158A TRP* 3.5 38.4 - - + -
159A LEU 3.7 6.7 - - - +
160A CYS* 3.9 7.8 - - - -
179A PRO* 4.5 9.4 - - + -
180A LEU* 5.2 5.2 - - + +
184A LEU 3.6 9.4 - - - +
185A ARG* 1.3 87.3 - - - +
187A ILE* 1.3 63.8 + - - +
224A MET* 4.0 14.6 - - - +
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Residues in contact with ILE 187 (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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110A PHE* 3.5 13.8 - - - -
114A CYS* 4.2 1.7 - - - -
126A LEU* 4.2 4.9 - - + -
159A LEU* 2.9 38.5 + - + +
160A CYS 4.7 0.2 - - - +
161A VAL* 4.0 9.9 - - + -
168A LEU* 3.7 26.5 - - + -
185A ARG 3.9 8.3 - - - +
186A PRO* 1.3 79.1 - - - +
188A PHE* 1.3 58.2 + - - +
220A PHE* 4.6 0.3 - - - -
221A VAL* 3.3 36.8 - - + +
224A MET* 3.7 19.3 - - + +
225A TYR* 3.6 40.2 - - + +
228A ALA* 4.4 1.8 - - + -
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Residues in contact with PHE 188 (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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110A PHE* 3.7 4.5 - - - -
114A CYS* 3.7 27.6 - - + -
115A LEU* 4.9 3.1 - - + -
140A PHE* 5.1 2.2 - + - -
144A PHE* 3.6 36.1 - + - -
158A TRP* 3.4 7.3 - - - +
159A LEU* 2.9 39.3 + - + +
187A ILE* 1.3 79.5 - - - +
189A THR* 1.3 78.9 + - - +
190A ALA* 4.6 0.2 - - + -
212A LEU* 4.3 13.5 - - + -
213A TRP* 3.7 20.4 - + - -
216A VAL* 3.5 37.9 - - + -
218A TRP* 5.0 3.1 - + + -
221A VAL* 3.8 22.4 - - + -
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Residues in contact with THR 189 (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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107A ASN 4.3 1.1 - - - +
110A PHE* 3.7 19.5 - - + -
111A PHE* 3.5 32.3 - - + +
114A CYS* 3.9 3.3 - - - +
156A TRP* 3.5 29.8 - - + +
157A THR 3.2 12.8 + - - -
158A TRP* 3.3 34.2 - - + -
188A PHE* 1.3 94.1 - - - +
190A ALA* 1.3 61.6 + - - +
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Residues in contact with ALA 190 (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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111A PHE* 3.8 5.4 - - - -
144A PHE* 3.7 23.5 - - + -
156A TRP* 3.5 4.6 - - - -
157A THR* 2.8 32.3 + - - +
188A PHE* 4.6 0.4 - - + -
189A THR* 1.3 73.3 + - - +
191A ASP* 1.3 63.8 - - - +
192A VAL* 3.4 3.6 + - + +
209A LEU* 3.8 13.7 - - + -
212A LEU* 3.5 26.9 - - + -
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Residues in contact with ASP 191 (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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58A HIS* 2.7 32.4 + - - -
108A HIS* 3.4 8.7 + - - -
111A PHE* 3.6 22.0 - - + -
155A GLY 3.7 0.3 - - - +
156A TRP* 3.4 32.0 - - + -
190A ALA* 1.3 70.9 - - - +
192A VAL* 1.3 57.8 + - - +
193A TRP* 3.2 31.7 + - - +
195A HIS* 3.6 2.8 + - - -
196A ALA* 3.5 17.1 - - + +
208A TYR* 2.7 31.5 + - - -
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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