Contacts of the strand formed by residues 174 - 182 (chain A) in PDB entry 2F24
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 LEU 174 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A LEU* 3.7 26.7 - - + -
92A ASP* 4.0 10.5 - - + +
99A PHE* 4.1 22.0 - - + -
101A PHE* 4.9 0.9 - - + -
165A LEU 3.5 3.1 - - - -
166A GLN* 3.6 30.1 - - + +
172A ARG 3.9 2.5 - - - +
173A SER* 1.3 74.8 - - - +
175A VAL* 1.3 62.0 + - - +
176A VAL* 4.2 0.4 - - + -
197A PHE 3.8 0.3 - - - +
198A LEU* 3.5 5.0 - - - +
199A SER* 2.8 34.2 + - - +
202A HIS* 3.7 15.0 - - - -
203A GLY* 3.7 23.8 - - - +
206A TRP* 4.0 21.4 - - + -
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Residues in contact with VAL 175 (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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164A CYS* 3.6 1.9 - - - +
165A LEU* 2.8 45.7 + - + +
167A LEU* 3.9 33.4 - - + -
174A LEU* 1.3 78.5 - - - +
176A VAL* 1.3 62.5 + - - +
177A PRO* 3.8 2.9 - - - +
196A CYS* 3.8 33.0 - - + -
197A PHE 3.4 3.8 - - - +
198A LEU* 3.9 14.8 - - + -
221A VAL* 3.9 12.3 - - + +
232A VAL* 4.8 4.9 - - + -
251A ASP 4.0 12.8 - - - +
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Residues in contact with VAL 176 (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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88A CYS* 5.2 0.2 - - + -
90A LEU* 5.3 1.6 - - + -
101A PHE* 3.7 37.0 - - + -
124A LEU* 6.4 0.2 - - + -
159A VAL* 3.8 25.4 - - + -
164A CYS* 3.9 16.6 - - + -
174A LEU 5.2 0.2 - - - -
175A VAL* 1.3 77.8 - - - +
177A PRO* 1.3 75.3 - - + +
178A ALA 3.7 0.2 + - - -
196A CYS* 3.4 3.8 - - - -
197A PHE* 2.9 47.5 + - + +
206A TRP* 3.7 21.8 - - + -
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Residues in contact with PRO 177 (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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159A VAL* 3.4 5.2 - - - +
160A GLY* 2.9 33.3 + - - +
162A GLY 5.5 0.2 - - - +
163A HIS 4.5 8.3 - - - +
164A CYS* 4.2 15.3 - - - -
175A VAL 3.8 7.4 - - - +
176A VAL* 1.3 88.1 - - + +
178A ALA* 1.3 61.9 + - - +
195A PHE 3.9 5.6 - - - +
196A CYS* 4.5 4.9 - - - -
219A CYS* 3.4 34.5 - - - +
220A GLN* 3.8 15.7 - - + -
221A VAL* 4.1 17.0 - - + +
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Residues in contact with ALA 178 (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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157A PHE* 5.9 0.2 - - + -
158A ALA 3.2 17.0 - - - +
159A VAL* 3.9 3.6 - - + +
160A GLY 4.4 1.8 - - - +
176A VAL 4.3 0.2 - - - +
177A PRO* 1.3 77.1 - - - +
179A TYR* 1.3 66.2 + - - +
194A ALA* 3.2 8.3 - - - +
195A PHE* 2.8 55.3 + - + +
197A PHE* 3.9 18.6 - - + -
219A CYS* 3.6 5.2 - - - -
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Residues in contact with TYR 179 (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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86A ASN* 4.8 2.8 + - - -
157A PHE* 3.3 4.6 - - - +
158A ALA* 3.0 59.9 + - + +
160A GLY 4.0 8.3 - - - -
178A ALA* 1.3 79.9 - - - +
180A ALA* 1.3 62.8 + - - +
181A TYR* 3.7 31.8 + + - -
192A PRO* 4.3 10.3 - - + -
193A SER 3.2 16.4 - - - +
194A ALA* 3.8 2.9 - - - -
195A PHE* 3.6 5.5 - - - -
217A LEU* 3.7 30.2 - - + +
218A GLU* 3.6 47.5 + - + +
219A CYS 5.0 0.4 - - - -
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Residues in contact with ALA 180 (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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154A TRP* 3.5 47.1 - - + +
156A THR 3.7 4.0 - - - -
157A PHE* 3.8 3.8 - - + +
179A TYR* 1.3 75.8 - - - +
181A TYR* 1.3 63.5 + - - +
182A ARG* 3.4 5.5 + - - +
191A ILE 3.5 0.3 - - - +
192A PRO* 3.1 4.4 - - - +
193A SER 2.9 30.1 + - - +
195A PHE* 3.8 8.2 - - + -
211A PHE* 4.0 7.2 - - + -
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Residues in contact with TYR 181 (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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154A TRP* 3.2 6.4 - - - -
155A SER* 3.0 43.5 + - - +
156A THR* 3.0 33.6 + - + +
157A PHE* 5.0 1.1 - - - -
179A TYR* 3.7 24.4 + + - -
180A ALA* 1.3 71.8 - - - +
182A ARG* 1.3 61.0 + - - +
190A PRO* 3.8 23.8 - - + -
191A ILE 3.6 3.1 - - - -
192A PRO* 3.6 28.9 - - + -
217A LEU* 3.7 19.1 - - + +
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Residues in contact with ARG 182 (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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153A GLU* 3.9 8.1 + - - +
154A TRP* 4.4 6.1 - - + +
180A ALA 3.8 9.9 - - - +
181A TYR* 1.3 71.6 - - - +
183A LYS* 1.3 60.4 + - - +
184A LEU* 3.0 48.8 + - + +
190A PRO* 3.3 4.2 - - - +
191A ILE 2.8 35.8 + - - +
193A SER* 4.0 17.8 + - - -
211A PHE* 3.2 55.5 - - + +
214A GLN* 4.7 10.7 + - - +
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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