Contacts of the strand formed by residues 171 - 178 (chain A) in PDB entry 3D14
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 ILE 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A LEU* 3.7 24.2 - - + -
163A ALA 3.5 4.0 - - - +
164A ARG* 3.8 33.9 - - + -
169A LYS 3.4 6.0 + - - +
170A PHE* 1.3 90.3 - - - +
172A LEU* 1.3 62.3 - - - +
225A TYR* 3.6 35.6 + - + +
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Residues in contact with LEU 172 (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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135A LEU* 4.0 18.4 - - + -
146A PHE* 3.9 23.8 - - + -
162A LEU* 3.5 11.4 - - - +
163A ALA* 2.9 34.2 + - + +
165A GLU* 3.7 18.4 - - + +
170A PHE* 3.3 26.7 - - + +
171A ILE* 1.3 74.5 - - - +
173A ALA* 1.3 77.5 + - - +
174A LEU* 4.3 8.3 - - + -
222A ILE* 3.6 27.8 - - + -
223A LEU 3.4 10.8 - - - +
224A GLU* 5.3 0.2 - - - -
225A TYR* 3.8 12.8 - - - +
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Residues in contact with ALA 173 (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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1A AK1 3.7 30.7 - - + +
152A LEU* 3.9 11.9 - - + -
160A VAL* 4.1 8.1 - - + -
161A TYR 3.3 10.5 - - - +
163A ALA* 4.7 0.2 - - - -
172A LEU* 1.3 82.6 - - - +
174A LEU* 1.3 62.7 + - - +
221A LEU 3.6 0.3 - - - +
223A LEU* 2.9 39.4 + - + +
224A GLU 4.3 0.9 - - - +
225A TYR* 4.2 2.2 - - - +
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Residues in contact with LEU 174 (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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143A LEU* 4.4 9.6 - - + -
146A PHE* 4.0 18.4 - - + -
148A ILE* 3.7 29.6 - - + -
159A ASN 3.9 1.0 - - - +
160A VAL* 3.3 4.1 - - - -
161A TYR* 2.8 45.1 + - + +
163A ALA* 3.8 15.9 - - + +
172A LEU* 4.3 5.4 - - + -
173A ALA* 1.3 74.5 - - - +
175A LYS* 1.3 62.1 + - - +
176A VAL* 4.0 7.1 + - + -
213A PHE* 4.1 12.6 - - + -
220A TYR* 4.3 9.6 - - + -
221A LEU 3.4 15.7 - - - +
222A ILE* 4.0 25.1 - - + -
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Residues in contact with LYS 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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1A AK1 3.1 45.1 + - - +
155A GLY* 4.7 8.5 - - - -
156A LYS 5.6 0.2 - - - +
157A PHE* 4.3 3.1 - - - +
158A GLY 3.9 29.8 + - - +
159A ASN 3.5 10.3 - - - +
160A VAL* 3.7 16.5 - - + +
174A LEU* 1.3 72.8 - - - +
176A VAL* 1.3 62.3 + - - +
177A LEU* 3.8 28.2 - - + +
219A VAL 3.6 1.7 - - - +
220A TYR* 3.3 6.8 - - - +
221A LEU* 2.9 42.2 + - + -
223A LEU* 4.0 18.9 - - + +
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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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158A GLY* 3.3 22.2 - - - -
159A ASN* 2.9 12.8 + - + +
161A TYR* 3.8 32.1 - - + -
174A LEU* 4.3 6.7 - - + +
175A LYS* 1.3 75.2 - - - +
177A LEU* 1.3 60.8 + - - +
178A PHE* 4.5 12.4 - - + -
218A ARG* 3.7 32.1 - - + -
219A VAL 3.7 2.7 - - - -
220A TYR* 3.7 27.4 - - + -
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Residues in contact with LEU 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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1A AK1 4.6 7.9 - - + -
157A PHE* 3.6 30.1 - - + +
175A LYS* 3.8 24.2 - - + +
176A VAL* 1.3 75.8 - - - +
178A PHE* 1.3 62.1 + - - +
182A LEU* 3.9 34.8 - - + -
191A LEU* 4.4 16.8 - - + -
218A ARG* 3.2 8.3 - - - +
219A VAL* 2.8 44.2 + - + +
221A LEU* 3.7 32.1 - - + -
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Residues in contact with PHE 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 4.3 6.1 + - - -
158A GLY* 5.7 3.4 - - - -
176A VAL* 4.5 12.8 - - + -
177A LEU* 1.3 78.6 - - - +
179A LYS* 1.3 67.1 + - - +
180A THR* 4.7 3.4 - - - +
181A GLN* 3.1 23.3 + - + +
182A LEU* 3.0 26.3 + - - +
217A THR* 3.8 9.4 - - - -
218A ARG* 3.7 38.8 - - + -
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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