Contacts of the strand formed by residues 165 - 171 (chain A) in PDB entry 1F6O
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 165 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A ILE* 3.2 7.7 - - - +
161A ILE* 2.8 43.3 + - + -
162A TYR* 4.8 1.8 - - + -
164A MET* 1.3 115.1 - - + +
166A PHE* 1.3 64.2 + - - +
197A ARG* 5.8 0.7 - - - -
219A SER* 3.0 29.2 - - - +
223A GLN* 3.7 28.0 - - + -
8D T 3.1 37.7 - + - -
9D T 3.2 41.8 + - - -
10D G 4.5 5.5 - - - -
18E A 5.2 0.4 - + - -
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Residues in contact with PHE 166 (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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158A VAL* 4.0 11.9 - - + -
159A TYR 3.4 2.2 - - - -
160A ILE* 3.5 37.2 - - + -
164A MET 4.9 8.7 - - - -
165A TYR* 1.3 79.5 - - - +
167A CYS* 1.3 64.1 + - - +
218A PRO 3.5 0.3 - - - +
219A SER* 3.0 30.3 + - - +
222A CYS* 3.5 25.3 - - + +
223A GLN* 5.8 6.7 - - + +
227A ILE 3.8 10.5 - - - +
228A ASN* 3.8 19.5 - - + -
229A LYS* 3.6 26.5 - - + -
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Residues in contact with CYS 167 (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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158A VAL* 3.2 23.8 - - - -
159A TYR* 3.0 35.7 + - + +
161A ILE* 3.9 23.6 - - - -
166A PHE* 1.3 80.4 - - - +
168A MET* 1.3 59.5 + - - +
169A ASN* 3.2 9.8 + - - +
180A LEU* 4.2 8.3 - - + -
218A PRO* 4.6 9.0 - - - -
219A SER* 4.2 4.5 - - - -
222A CYS* 4.1 1.6 - - - -
7D YRR 4.0 23.3 - - - -
8D T 4.4 4.3 - - - -
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Residues in contact with MET 168 (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 LEU* 3.8 36.8 - - + -
156A LEU* 3.9 28.9 - - + -
157A TYR 4.0 1.1 - - - -
158A VAL* 4.3 15.5 - - + -
167A CYS* 1.3 71.1 - - - +
169A ASN* 1.3 67.1 + - - +
170A ILE* 4.1 6.3 - - + -
180A LEU* 3.3 5.5 - - - +
181A LEU* 3.1 50.5 + - + +
218A PRO 4.8 2.0 + - - -
221A LEU* 4.7 10.1 - - + -
222A CYS* 3.7 19.0 - - - -
227A ILE* 4.1 25.4 - - + -
236A LEU* 4.8 4.7 - - + -
242A VAL* 5.7 1.8 - - + -
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Residues in contact with ASN 169 (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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127A TYR* 4.9 3.1 - - - -
156A LEU* 3.4 8.1 - - - +
157A TYR* 2.8 58.1 + - + +
159A TYR* 3.6 25.2 - - - -
167A CYS 3.2 15.6 + - - -
168A MET* 1.3 75.1 - - - +
170A ILE* 1.3 67.4 + - - +
178A CYS* 4.1 18.1 - - + -
179A VAL 3.0 8.4 - - - +
180A LEU* 3.3 29.4 + - - +
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Residues in contact with ILE 170 (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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91A PHE* 3.7 18.6 - - + -
98A LEU* 4.8 0.9 - - + -
102A PHE* 3.9 20.4 - - + -
154A GLY* 3.7 23.6 - - - +
155A THR 3.6 2.7 - - - -
156A LEU* 3.8 13.7 - - + -
168A MET* 4.1 13.2 - - + -
169A ASN* 1.3 80.0 - - - +
171A SER* 1.3 73.8 + - - +
172A SER 3.4 0.2 + - - -
178A CYS* 3.8 2.7 - - - -
179A VAL* 2.7 41.3 + - - +
181A LEU* 3.8 35.7 - - + -
236A LEU* 4.1 11.9 - - + -
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Residues in contact with SER 171 (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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91A PHE 4.3 0.2 - - - +
98A LEU* 4.2 2.5 - - - +
148A GLY 3.4 21.8 + - - -
149A MET 3.5 0.2 + - - -
151A MET 3.0 18.1 + - - -
152A LYS 3.9 9.1 + - - -
153A PRO* 3.4 0.3 - - - +
154A GLY 2.9 22.4 + - - -
155A THR 2.8 20.8 + - - -
157A TYR* 5.3 1.2 - - - +
169A ASN* 4.1 0.6 - - - +
170A ILE* 1.3 77.2 - - - +
172A SER* 1.3 58.6 + - - +
177A ALA 4.4 0.4 - - - -
178A CYS* 3.7 11.4 - - - +
1001A NA 2.6 24.4 - - - -
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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