Contacts of the strand formed by residues 170 - 174 (chain A) in PDB entry 2L3S
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 TRP 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A PHE* 5.1 10.5 - + - -
151A ASP* 6.3 1.1 - - + -
165A LYS* 4.7 0.3 - - - -
166A PRO* 5.0 0.5 - - - +
167A GLU* 2.9 25.4 + - + +
168A GLU 4.2 0.8 - - - +
169A GLN* 1.3 88.9 + - + +
171A TRP* 1.3 79.4 + - - +
182A MET* 4.2 32.3 - - + -
183A ILE* 3.1 31.9 - - - -
184A PRO* 3.2 34.8 - - + -
185A VAL* 3.7 0.7 - - - -
234A LEU* 5.9 4.7 - - + -
236A ASN 3.9 5.8 - - - -
237A GLY 3.5 24.2 - - - -
238A PRO* 3.4 13.2 + - + -
239A PHE* 2.9 34.6 - + - -
297A GLN* 4.2 6.5 - - - -
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Residues in contact with TRP 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A VAL* 4.5 16.8 - - + -
162A ILE* 4.6 18.6 - - + -
164A ASP 4.3 0.7 - - - -
165A LYS* 2.5 55.9 - - + +
166A PRO* 5.2 0.9 - - - -
167A GLU 3.1 6.6 + - - -
168A GLU* 3.8 13.5 + - + +
170A TRP* 1.3 92.2 + - - +
172A ASN* 1.3 59.1 + - - +
182A MET* 4.5 3.8 - - - -
183A ILE* 2.7 53.9 + - + +
185A VAL* 3.1 37.7 - - + -
188A VAL* 4.8 6.3 - - + -
190A LYS* 3.7 40.8 - - + -
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Residues in contact with ASN 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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162A ILE* 3.7 4.3 - - - +
163A ARG* 3.0 29.5 + - - +
164A ASP* 2.8 38.9 + - + +
166A PRO* 4.7 7.5 - - + +
171A TRP* 1.3 69.4 - - - +
173A ALA* 1.3 67.6 + - - +
180A ARG* 4.2 9.4 - - - +
181A GLY* 3.5 23.9 + - - +
182A MET* 4.3 14.5 - - + +
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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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152A LEU* 3.4 15.8 - - + +
160A LEU* 3.8 13.2 - - + -
161A LYS 3.3 9.2 - - - +
162A ILE* 4.2 6.1 - - + +
163A ARG* 5.3 2.0 - - - -
171A TRP 3.2 1.8 + - - -
172A ASN* 1.3 76.0 - - - +
174A GLU* 1.3 60.7 + - - +
180A ARG* 3.5 3.5 - - - +
181A GLY 3.0 31.2 + - - +
183A ILE* 3.4 32.8 - - + -
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Residues in contact with GLU 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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152A LEU* 3.5 4.5 - - - -
159A ILE 4.5 0.2 - - - +
160A LEU* 3.4 22.0 - - - -
161A LYS* 2.8 23.8 + - + +
163A ARG* 4.9 13.2 - - + -
173A ALA* 1.3 74.3 - - - +
175A ASP* 1.3 73.2 + - - +
178A GLY* 4.2 14.8 - - - -
179A LYS 3.0 27.1 - - - +
180A ARG* 3.8 26.9 + - + +
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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