Contacts of the strand formed by residues 199 - 208 (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 GLN 199 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A VAL* 6.3 2.2 - - + -
194A CYS 3.6 0.7 - - - +
195A LEU* 3.6 4.2 - - - +
196A VAL* 2.9 33.2 + - - +
197A ASN 4.5 5.2 - - - +
198A GLY* 1.3 92.1 + - - +
200A TYR* 1.3 70.2 + - - +
201A ALA* 3.7 1.8 + - + +
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Residues in contact with TYR 200 (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* 4.2 22.2 - + + -
113A VAL* 4.4 12.1 + - - +
126A PRO* 4.9 4.4 - - - +
128A TYR* 3.5 33.2 - + - -
193A HIS* 3.7 28.3 - - + +
194A CYS 3.4 5.8 - - - -
195A LEU* 3.7 49.0 - - + +
198A GLY 5.8 0.4 - - - -
199A GLN* 1.3 81.1 + - - +
201A ALA* 1.3 59.2 + - - +
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Residues in contact with ALA 201 (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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113A VAL* 3.3 23.8 - - + +
114A LEU 4.3 1.6 - - - -
115A PRO* 4.2 11.9 - - + -
193A HIS* 3.3 3.4 - - - -
194A CYS 2.8 30.8 + - - +
196A VAL* 5.7 2.5 - - + -
199A GLN* 3.7 2.9 + - + +
200A TYR* 1.3 74.5 - - - +
202A VAL* 1.3 65.4 + - - +
203A HIS* 3.2 24.9 + - + +
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Residues in contact with VAL 202 (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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14A SER* 4.4 5.8 - - - +
33A THR* 3.8 27.8 - - + +
41A MET* 4.0 12.3 - - + -
112A GLY* 4.6 4.9 - - - -
113A VAL 2.8 19.6 + - - +
114A LEU* 4.0 7.1 - - + +
115A PRO* 3.1 19.3 - - - +
191A PRO* 3.6 26.2 - - + -
192A LEU 3.3 4.0 - - - +
193A HIS* 4.1 12.3 - - - +
201A ALA* 1.3 72.7 - - - +
203A HIS* 1.3 58.4 + - - +
204A GLY 3.4 22.4 - - - +
226A VAL* 3.5 9.4 - - + +
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Residues in contact with HIS 203 (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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115A PRO* 3.5 31.5 - - + +
119A THR* 4.1 19.7 + - + +
121A LEU* 3.5 36.8 - - + +
173A VAL* 3.9 9.2 - - + +
192A LEU* 2.9 7.8 + - + -
194A CYS* 3.7 26.5 - - + -
196A VAL* 3.6 19.0 - - + +
201A ALA* 3.4 27.2 - - + +
202A VAL* 1.3 74.5 - - - +
204A GLY* 1.3 59.8 + - - +
225A ARG* 3.7 8.5 - - + +
226A VAL* 2.9 23.9 + - - -
227A SER* 4.5 1.1 + - - -
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Residues in contact with GLY 204 (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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173A VAL* 5.0 0.9 - - - -
191A PRO* 3.4 1.7 - - - +
192A LEU* 3.0 35.4 + - - +
202A VAL* 3.4 14.0 - - - +
203A HIS* 1.3 81.6 - - - +
205A VAL* 1.3 64.0 + - - -
206A THR 4.1 0.2 - - - -
223A PHE* 3.8 14.8 - - - -
224A THR 3.3 8.3 - - - -
226A VAL* 3.8 1.6 - - - -
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Residues in contact with VAL 205 (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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33A THR* 5.9 0.2 - - - +
41A MET* 3.9 29.2 - - + -
42A THR 3.6 24.0 - - - +
43A ALA* 3.7 8.1 - - + +
93A ASP 4.2 3.4 - - - +
94A ILE* 4.7 7.9 - - + -
189A GLY* 3.5 27.1 - - - +
190A GLY 3.3 3.8 - - - +
204A GLY* 1.3 74.6 - - - +
206A THR* 1.3 63.5 + - - +
207A SER* 3.2 0.5 + - - -
223A PHE* 3.2 2.3 - - - +
224A THR* 2.8 42.9 + - - +
226A VAL* 3.8 17.5 - - + -
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Residues in contact with THR 206 (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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43A ALA* 3.8 7.3 - - - +
129A ILE* 3.8 10.2 - - + +
183A GLY* 5.2 0.7 - - - -
187A ASP* 3.4 28.8 + - + +
188A SER* 3.4 17.0 - - - +
189A GLY 2.8 23.6 + - - +
190A GLY 2.8 16.9 + - - -
205A VAL* 1.3 71.1 - - - +
207A SER* 1.3 61.3 + - - +
221A THR* 4.2 20.4 - - + -
223A PHE* 3.2 25.1 - - + -
261A XE 4.1 14.1 - - - -
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Residues in contact with SER 207 (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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45A HIS* 3.1 23.3 + - - -
88A VAL* 3.4 6.4 + - - +
93A ASP* 2.6 30.7 + - - +
172A MET* 6.1 0.6 - - - +
188A SER* 3.9 4.4 + - - -
205A VAL 3.2 7.4 + - - -
206A THR* 1.3 75.8 - - - +
208A PHE* 1.3 80.3 + - - +
222A VAL* 2.8 16.1 + - - -
223A PHE 4.3 0.9 - - - -
224A THR* 4.0 15.5 - - - -
261A XE 4.6 0.9 - - - -
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Residues in contact with PHE 208 (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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88A VAL* 3.7 28.5 - - + -
89A ALA* 4.6 1.3 - - - -
164A TRP* 3.7 27.8 - + - -
167A THR* 3.9 17.7 - - + -
168A VAL* 4.6 1.8 - - + -
172A MET* 4.1 16.4 - - + -
206A THR* 4.8 0.4 - - - +
207A SER* 1.3 97.1 - - - +
209A VAL* 1.3 69.4 - - - +
221A THR* 3.9 1.1 - - - +
222A VAL* 2.8 66.1 + - + +
250A GOL 3.6 30.5 - - - -
261A XE 4.1 7.3 - - - -
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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