Contacts of the strand formed by residues 176 - 179 (chain A) in PDB entry 1LCY
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 PRO 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A VAL* 4.2 8.3 - - + -
51A GLY 4.3 1.1 - - - +
52A PHE* 3.5 32.5 - - + -
110A LEU* 3.8 22.4 - - + -
125A VAL 3.4 2.4 - - - +
127A MET* 3.0 42.0 + - + +
175A GLY* 1.3 85.1 - - - +
177A LEU* 1.3 59.4 + - - +
178A VAL* 3.6 9.8 + - + -
184A VAL* 3.8 22.4 - - + -
186A GLY 3.5 5.2 - - - +
188A ASN* 3.3 3.5 + - - -
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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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124A VAL* 3.9 26.0 - - + -
125A VAL 3.5 16.8 - - - +
126A ALA* 4.0 8.7 - - + +
162A ILE* 3.8 16.4 - - + -
164A THR* 4.3 20.2 - - + -
166A ALA* 4.9 0.7 - - + -
168A ILE* 5.4 0.7 - - + -
176A PRO* 1.3 70.9 - - - +
178A VAL* 1.3 58.8 + - - +
184A VAL* 3.7 1.6 - - - -
185A ILE* 3.0 50.6 + - + +
186A GLY 2.8 21.1 + - - +
188A ASN* 3.3 15.8 + - - +
199A ALA* 3.7 21.5 - - + -
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Residues in contact with VAL 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 3.7 16.2 - - + -
24A THR* 4.0 10.5 - - + +
110A LEU* 4.8 0.7 - - + -
124A VAL* 3.1 9.3 - - - -
125A VAL* 2.8 39.1 + - - +
127A MET* 4.1 12.8 - - + -
176A PRO* 3.9 29.8 - - + +
177A LEU* 1.3 76.7 - - - +
179A ASN* 1.3 73.8 + - - +
182A GLY* 3.3 32.5 - - - +
183A GLU 3.3 5.6 - - - +
184A VAL* 4.7 6.1 - - + -
185A ILE* 4.6 0.2 - - - -
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Residues in contact with ASN 179 (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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20A VAL* 3.5 6.6 - - - +
118A VAL* 5.8 0.8 - - + +
122A GLU* 4.1 19.3 + - - +
123A PHE 3.9 9.4 - - - +
124A VAL* 4.0 6.3 - - + -
177A LEU 4.3 0.4 + - - -
178A VAL* 1.3 81.2 - - - +
180A LEU* 1.3 61.4 + - - +
181A ASP* 2.8 19.2 + - - +
182A GLY 3.0 11.6 + - - -
183A GLU* 2.9 52.3 + - - +
185A ILE* 3.6 25.6 - - + +
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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