Contacts of the strand formed by residues 174 - 178 (chain A) in PDB entry 6APL
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 174 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A PHE* 3.6 36.4 - + - -
147A LYS* 3.5 30.9 + - - -
149A ILE* 4.1 19.5 - - + -
150A ARG 3.2 3.1 + - - -
151A CYS* 3.3 17.0 - - + -
152A ALA 2.9 24.2 + - - -
172A HIS* 3.7 3.3 - - - +
173A ASP* 1.3 100.4 - - + +
175A VAL* 1.3 66.4 + - - +
176A PHE* 4.8 0.4 - - + -
195A SER* 3.3 21.8 - - - +
196A PHE* 4.1 12.6 - + + -
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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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152A ALA* 3.2 6.5 - - + +
154A VAL* 3.8 26.9 - - + -
169A ILE* 3.8 26.7 - - + +
172A HIS 4.6 2.0 - - - +
174A TYR* 1.3 80.0 - - - +
176A PHE* 1.3 66.0 + - - +
177A ARG* 4.1 9.2 - - + +
193A LYS* 3.4 52.5 - - + +
194A THR* 4.0 1.4 - - - -
195A SER* 2.8 32.1 + - - +
196A PHE 3.0 10.0 + - - +
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Residues in contact with PHE 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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137A LEU* 4.2 20.4 - - + -
138A PHE* 4.4 2.0 - + - -
151A CYS* 3.9 29.4 - - + -
152A ALA 2.6 19.0 + - - +
153A VAL* 4.0 25.7 - - + +
154A VAL* 2.8 32.9 + - - +
174A TYR* 4.8 1.6 - - + -
175A VAL* 1.3 73.6 - - - +
177A ARG* 1.3 62.2 + - - +
178A LEU* 4.8 1.3 - - - -
196A PHE* 3.5 39.7 - + + +
228A ILE* 4.5 0.2 - - + -
309A MSE 3.7 36.6 - - + -
312A THR* 4.7 7.2 - - + -
313A ALA* 3.9 18.6 - - + -
316A THR* 4.4 0.4 - - - -
317A CYS* 4.4 4.7 - - - -
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Residues in contact with ARG 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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154A VAL* 3.7 27.1 - - + +
169A ILE* 4.1 5.1 - - - +
170A ASP* 4.1 2.8 + - - -
175A VAL* 4.2 5.8 - - + -
176A PHE* 1.3 78.1 - - - +
178A LEU* 1.3 69.4 + - - +
181A ALA* 3.8 24.7 - - + +
183A ILE* 4.0 14.1 - - - +
190A VAL* 3.0 41.2 + - - +
191A GLY* 3.4 21.4 - - - -
192A THR 3.6 1.0 - - - +
193A LYS 2.9 19.6 + - - +
194A THR* 3.0 33.8 + - + -
196A PHE 2.9 10.0 + - - +
197A TYR* 3.2 9.4 - - + -
198A GLY 2.9 22.7 + - - -
220A PRO* 4.9 1.1 - - + -
309A MSE 4.4 2.1 - - - +
337A TYR* 5.0 2.4 + - - -
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Residues in contact with LEU 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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153A VAL* 4.3 10.5 - - + -
154A VAL 3.7 21.5 + - - +
155A GLY* 4.4 6.7 - - - -
156A ASN* 2.9 36.7 + - - +
177A ARG* 1.3 82.7 - - - +
179A ASN* 1.3 74.7 + - + +
180A GLY 3.3 0.2 + - - -
181A ALA* 3.5 6.1 + - - +
197A TYR* 3.6 4.6 - - - -
198A GLY* 3.1 16.4 - - - +
305A THR* 4.0 14.4 - - + -
306A GLY* 4.0 25.4 - - - +
309A MSE 3.7 26.9 - - + -
325A PHE* 4.9 0.4 - - + -
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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