Contacts of the strand formed by residues 58 - 62 (chain G) in PDB entry 1LQM
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 VAL 58 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56G VAL* 4.0 0.7 - - - +
57G LYS* 1.3 89.3 - - + +
59G VAL* 1.3 72.3 + - - +
60G ILE* 4.4 0.2 - - + -
118G GLY 3.1 6.9 + - - +
119G VAL* 3.5 21.0 - - + -
120G LEU* 3.1 23.3 + - - +
160G VAL* 3.1 22.4 - - + +
162G LEU* 3.5 33.4 - - + -
206G ALA* 4.2 14.6 - - + -
210G LEU* 4.4 11.4 - - + -
218G ILE* 4.6 10.8 - - + -
220G TRP* 4.5 6.3 - - + -
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Residues in contact with VAL 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56G VAL* 3.5 23.1 - - + -
58G VAL* 1.3 81.7 - - - +
60G ILE* 1.3 62.6 + - - +
61G LEU* 3.4 28.5 + - + +
120G LEU* 3.7 24.7 - - + +
122G LEU* 5.2 4.7 - - + -
149G ILE* 6.0 1.3 - - + -
152G ILE* 4.6 9.2 - - + -
159G VAL* 4.2 10.8 - - + -
160G VAL 2.8 12.1 + - - +
161G PHE* 3.7 22.1 - - + +
162G LEU 3.0 25.8 + - - +
163G LEU* 4.9 0.3 - - - +
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Residues in contact with ILE 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58G VAL* 4.4 0.4 - - + -
59G VAL* 1.3 76.6 - - - +
61G LEU* 1.3 66.0 + - - +
62G GLY 3.9 0.3 + - - -
76G ALA* 4.3 1.6 - - - +
77G PHE* 3.5 29.6 - - + -
92G MET* 5.5 1.1 - - + -
114G TRP* 4.2 17.7 - - + -
119G VAL* 3.7 26.0 - - + +
120G LEU 3.1 6.7 + - - +
121G LEU* 3.9 20.3 - - + -
122G LEU 3.4 22.5 + - - +
162G LEU* 3.9 32.1 - - + +
164G TRP* 3.6 26.9 - - + -
203G PHE* 5.1 0.7 - - + -
220G TRP* 4.7 4.9 - - + -
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Residues in contact with LEU 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59G VAL* 3.4 30.7 - - + +
60G ILE* 1.3 77.1 - - - +
62G GLY* 1.3 61.3 + - - +
77G PHE* 3.6 16.9 - - - -
122G LEU* 3.5 21.1 - - + +
124G THR* 4.4 9.6 - - + -
149G ILE* 4.0 26.7 - - + -
161G PHE* 5.4 2.2 - - + -
162G LEU 4.0 6.7 + - - +
163G LEU* 4.4 15.3 - - + -
164G TRP* 5.3 6.1 + - - +
168G ALA* 4.3 27.7 - - + +
171G LYS* 4.0 23.1 - - + -
172G GLY 5.5 0.4 - - - +
187G HIS* 6.1 0.5 - - - -
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Residues in contact with GLY 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60G ILE 3.9 1.0 + - - -
61G LEU* 1.3 75.6 - - - +
63G GLN* 1.3 65.2 + - - -
76G ALA* 4.1 8.1 - - - +
77G PHE* 4.3 11.9 - - - -
122G LEU 3.3 8.7 + - - +
123G ASN* 3.5 14.8 - - - -
124G THR* 2.9 28.2 + - - +
167G HIS* 6.1 0.2 - - - -
187G HIS* 6.3 0.4 - - - -
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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