Contacts of the helix formed by residues 171 - 177 (chain A) in PDB entry 1LC9
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 SER 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A VAL* 4.9 1.8 - - - +
169A TYR 3.7 1.0 + - - -
170A ARG* 1.4 72.5 - - - +
172A PRO* 1.3 74.2 - - - +
173A GLU* 3.5 20.4 - - - -
174A VAL* 2.7 34.8 + - - +
175A LEU* 3.3 3.4 + - - +
185A VAL* 3.2 29.0 + - - +
188A TRP* 2.8 29.3 - - - +
275A ARG* 4.0 0.7 - - - -
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Residues in contact with PRO 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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170A ARG 3.9 0.6 - - - -
171A SER* 1.3 82.0 - - - +
173A GLU* 1.3 70.5 + - - +
175A LEU* 3.2 10.4 + - + +
176A LEU* 2.8 38.9 + - + +
188A TRP* 3.7 23.6 - - + -
213A LEU* 4.5 8.1 - - + -
216A ILE* 4.8 9.6 - - + -
217A PHE* 6.0 2.0 - - + -
228A TRP* 4.3 13.0 - - + -
270A TYR* 4.2 22.9 - - + -
275A ARG* 3.1 25.1 - - - +
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Residues in contact with GLU 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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171A SER* 3.5 10.2 - - - -
172A PRO* 1.3 78.8 - - - +
174A VAL* 1.3 61.4 + - - +
176A LEU* 3.4 2.9 + - - +
177A GLY 3.1 3.5 + - - -
178A SER* 2.9 44.2 + - - -
180A ARG 5.3 2.5 - - - +
181A TYR* 5.0 10.9 - - + +
182A SER 5.8 0.3 + - - -
184A PRO* 4.8 0.3 - - - +
185A VAL* 3.7 12.6 + - - +
228A TRP* 3.7 26.7 - - + -
270A TYR 3.8 1.9 - - - +
272A PRO* 3.9 21.5 - - + +
275A ARG* 2.7 48.6 + - - -
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Residues in contact with VAL 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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127A ARG* 5.4 2.2 - - - +
162A HIS 5.5 2.5 - - - +
163A GLU* 5.7 3.4 - - - +
164A VAL* 3.9 31.9 - - + +
165A VAL* 5.6 2.0 - - + -
170A ARG* 3.7 27.4 - - + -
171A SER* 2.7 31.4 + - - +
173A GLU* 1.3 78.4 - - - +
175A LEU* 1.3 70.5 + - + +
177A GLY* 2.9 14.4 + - - -
178A SER 4.9 2.7 - - - +
181A TYR* 4.7 17.2 - - + +
185A VAL* 5.6 3.5 - - + +
236A ASP* 4.5 0.5 - - - +
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Residues in contact with LEU 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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167A LEU* 4.4 5.2 - - + -
170A ARG* 3.5 47.8 - - + +
171A SER 3.6 9.2 - - - +
172A PRO* 3.2 2.9 + - + +
174A VAL* 1.3 84.3 - - + +
176A LEU* 1.3 52.6 + - - +
209A GLU* 4.4 23.4 - - + +
212A GLN* 3.5 32.8 - - + -
213A LEU* 3.1 42.7 - - + +
216A ILE* 4.1 10.1 - - + -
236A ASP* 2.8 24.1 - - - +
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Residues in contact with LEU 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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172A PRO* 2.8 23.0 + - + +
173A GLU 3.7 1.3 - - - +
175A LEU* 1.3 74.7 - - - +
177A GLY* 1.3 59.3 + - - +
213A LEU* 3.9 25.8 - - + -
217A PHE* 4.8 10.1 - - + -
223A PRO* 5.5 7.0 - - + -
228A TRP* 3.7 27.4 - - + -
231A VAL* 5.2 6.5 - - + +
234A LEU* 3.0 38.1 - - + +
235A GLN 3.9 3.5 + - - -
236A ASP* 2.7 33.5 + - + +
237A TYR* 4.6 22.2 - - + +
241A PHE* 4.8 4.5 - - + -
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Residues in contact with GLY 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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174A VAL 2.9 15.3 + - - -
175A LEU 3.2 0.8 - - - -
176A LEU* 1.3 78.5 - - - +
178A SER* 1.3 68.9 + - - +
179A ALA* 3.2 2.8 + - - -
235A GLN* 4.1 26.6 + - - +
236A ASP* 3.4 13.2 - - - -
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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