Contacts of the strand formed by residues 127 - 131 (chain A) in PDB entry 1L1G
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 CYS 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A LEU* 4.4 0.2 - - - -
125A SER 3.5 5.1 + - - -
126A PRO* 1.3 75.0 - - - +
128A TYR* 1.3 66.7 + - - +
149A TYR* 3.5 10.3 - - - -
150A LEU 2.9 38.0 + - - +
152A THR* 3.6 26.7 - - - -
192A LEU* 3.7 13.0 - - + -
193A HIS 3.1 6.7 - - - +
194A CYS* 2.1 48.0 - - - -
200A TYR* 5.2 0.4 - - - -
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Residues in contact with TYR 128 (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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12A TRP* 4.0 26.2 - + + -
126A PRO* 6.2 0.9 - - + -
127A CYS* 1.3 77.0 - - - +
129A ILE* 1.3 63.4 + - - +
130A THR* 4.9 0.2 - - + -
147A GLN* 3.5 33.9 + - + -
148A ALA* 3.2 20.2 - - - -
149A TYR* 3.6 38.1 - + + +
192A LEU* 3.9 4.0 - - - -
193A HIS* 2.8 38.3 + - + -
200A TYR* 3.5 31.4 - + - -
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Residues in contact with ILE 129 (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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1A VAL* 4.2 12.2 - - + +
128A TYR* 1.3 73.7 - - - +
130A THR* 1.3 73.1 + - - +
147A GLN* 3.2 5.0 - - - -
148A ALA* 2.9 48.5 + - + +
150A LEU* 3.6 25.5 - - + +
183A GLY* 3.5 32.1 - - - +
187A ASP* 4.5 6.1 - - + +
191A PRO 3.8 13.0 - - - +
192A LEU* 4.0 8.1 - - + +
206A THR* 3.8 13.0 - - + +
221A THR* 4.3 1.6 - - + -
223A PHE* 3.8 24.5 - - + -
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Residues in contact with THR 130 (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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1A VAL* 4.1 4.9 - - - -
12A TRP* 3.4 41.3 - - + +
15A GLN* 2.6 32.4 + - - +
128A TYR* 4.0 0.6 + - + +
129A ILE* 1.3 88.6 - - - +
131A GLY* 1.3 59.4 + - - +
145A LEU* 4.3 6.7 - - - -
146A GLN 3.1 11.2 - - - +
147A GLN* 3.9 4.3 - - + -
187A ASP* 4.3 5.4 - - - +
190A GLY* 4.8 3.6 - - - -
191A PRO* 3.3 14.2 + - - +
193A HIS* 2.7 29.0 + - + +
206A THR* 5.4 0.2 + - - -
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Residues in contact with GLY 131 (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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1A VAL* 3.7 3.4 - - - +
15A GLN* 4.1 7.0 - - - -
130A THR* 1.3 77.4 - - - +
132A TRP* 1.3 59.4 - - - -
133A GLY 3.9 0.2 + - - -
145A LEU* 3.4 16.3 - - - +
146A GLN* 2.9 36.7 + - - +
186A GLY 5.5 0.2 - - - -
187A ASP* 3.3 17.3 - - - -
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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