Contacts of the strand formed by residues 161 - 169 (chain A) in PDB entry 4DNL
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 161 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A GLY* 1.3 76.3 - - - +
162A ILE* 1.3 62.0 + - - +
180A ALA* 3.2 6.2 - - - +
181A LYS* 2.9 65.1 + - + +
182A ASN* 3.0 30.5 - - - +
274A TRP* 3.7 33.4 - - + +
275A TYR 3.1 15.5 - - - +
277A LEU* 3.7 7.9 - - - +
290A ILE* 3.8 27.1 - - + -
293A GLY 5.3 7.8 + - - -
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Residues in contact with ILE 162 (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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161A ARG* 1.3 75.3 - - - +
163A TYR* 1.3 63.8 + - - +
164A LEU* 3.5 30.0 + - + -
177A VAL* 4.3 13.0 - - + -
179A ASP 3.5 13.9 - - - +
180A ALA* 4.4 6.1 - - + -
196A VAL* 4.4 4.0 - - + -
223A TRP* 4.8 0.7 - - + -
242A VAL* 4.2 15.3 - - + -
244A ILE* 4.0 20.6 - - + -
259A LEU* 3.9 15.3 - - + -
273A GLY 3.6 1.2 - - - +
274A TRP* 3.4 6.3 - - - -
275A TYR* 2.9 40.6 + - + +
277A LEU* 3.7 23.6 - - + -
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Residues in contact with TYR 163 (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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162A ILE* 1.3 72.5 - - - +
164A LEU* 1.3 66.6 + - - +
165A LYS* 3.9 38.1 + - + -
178A ARG* 3.1 72.3 + - + +
179A ASP* 2.8 28.8 + - - +
272A SER* 4.0 4.5 + - - -
273A GLY* 3.3 33.1 + - - -
274A TRP* 3.6 24.4 - + + -
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Residues in contact with LEU 164 (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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162A ILE* 3.5 31.6 - - + -
163A TYR* 1.3 83.2 - - - +
165A LYS* 1.3 68.3 + - - +
166A ALA* 5.8 0.9 - - + -
175A VAL* 5.1 5.6 - - + -
176A THR 3.4 4.9 - - - +
177A VAL* 3.9 26.9 - - + -
242A VAL* 4.0 21.3 - - + -
259A LEU* 3.8 30.7 - - + -
261A PHE* 3.9 17.0 - - + -
271A ALA* 4.2 1.5 - - + -
272A SER* 3.3 4.2 + - - -
273A GLY 3.0 31.9 + - - +
275A TYR* 4.3 7.6 - - + -
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Residues in contact with LYS 165 (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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163A TYR* 3.9 23.9 + - + -
164A LEU* 1.3 80.6 - - - +
166A ALA* 1.3 61.3 + - - +
167A GLU* 6.0 0.9 - - + -
174A HIS 4.4 0.4 - - - -
175A VAL* 3.2 5.4 - - - +
176A THR* 2.8 49.0 + - + +
271A ALA 3.3 6.3 - - - +
272A SER* 3.1 25.8 - - - +
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Residues in contact with ALA 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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164A LEU* 5.8 1.6 - - + -
165A LYS* 1.3 76.2 - - - +
167A GLU* 1.3 64.3 + - - +
173A LEU* 4.7 0.2 - - - -
174A HIS 3.1 9.9 - - - +
175A VAL* 4.5 4.3 - - + -
240A LEU* 4.3 15.7 - - + -
261A PHE* 5.2 3.8 - - + -
266A LEU* 3.9 25.3 - - + +
270A PRO* 3.4 3.1 - - - +
271A ALA* 2.8 44.9 + - + +
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Residues in contact with GLU 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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165A LYS* 6.0 0.7 - - + -
166A ALA* 1.3 77.8 - - - +
168A VAL* 1.3 66.2 + - - +
169A ALA* 4.1 17.2 + - - +
172A LYS 3.8 0.3 - - - +
173A LEU* 3.4 4.0 - - - +
174A HIS* 2.8 52.1 + - + +
266A LEU* 4.6 4.7 - - - +
270A PRO* 4.0 17.9 - - + -
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Residues in contact with VAL 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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167A GLU* 1.3 80.7 - - - +
169A ALA* 1.3 65.9 + - - +
171A GLU* 4.9 6.5 - - - +
172A LYS 3.3 7.6 - - - +
173A LEU* 3.8 18.2 - - + -
231A LEU* 3.8 31.0 - - + -
263A VAL* 4.1 22.0 - - + +
266A LEU* 4.2 12.0 + - + +
267A MSE 3.7 35.3 - - + +
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Residues in contact with ALA 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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167A GLU* 4.1 14.8 + - - +
168A VAL* 1.3 74.8 - - - +
170A ASP* 1.3 74.6 + - + +
171A GLU 3.3 2.7 - - - -
172A LYS* 2.9 24.3 + - - +
174A HIS* 4.5 12.7 + - + +
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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