Contacts of the strand formed by residues 192 - 198 (chain L) in PDB entry 4XX1
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 TYR 192 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118L LEU* 4.6 5.0 - - + +
133L LEU* 3.5 27.8 - - + -
149L TRP* 5.3 3.4 - + + -
150L LYS 3.7 3.6 - - - -
151L ALA* 3.7 21.4 - - + +
156L VAL* 5.2 1.6 - - + -
179L LEU* 3.9 15.0 - - + -
181L LEU* 3.4 25.0 - - + +
185L GLN 2.4 31.4 + - - -
186L TRP* 3.2 37.2 - + - +
189L HIS* 3.4 28.4 - - + -
191L SER* 1.3 81.5 - - - +
193L SER* 1.3 62.4 + - - +
206L THR* 3.2 7.0 - - - -
207L VAL* 3.1 34.5 + - + +
209L PRO* 5.9 0.4 - - + -
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Residues in contact with SER 193 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118L LEU* 4.8 2.0 - - - -
149L TRP* 3.5 15.9 - - - -
150L LYS* 3.0 40.3 + - - -
152L ASP 5.4 4.7 - - - -
191L SER* 5.8 0.7 - - - -
192L TYR* 1.3 79.3 - - - +
194L CYS* 1.3 73.2 + - - +
195L GLN* 5.0 1.4 - - - +
204L GLU* 4.4 9.4 + - - +
205L LYS 3.5 6.1 + - - -
206L THR* 3.3 23.2 - - - +
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Residues in contact with CYS 194 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116L VAL* 4.8 6.5 - - + -
118L LEU* 3.6 13.9 - - + +
135L CYS* 2.0 53.8 - - - -
147L VAL* 5.5 1.3 - - + -
148L ALA 3.9 5.8 - - - +
149L TRP* 3.5 22.0 - - + -
193L SER* 1.3 76.2 + - - +
195L GLN* 1.3 64.1 + - - +
196L VAL* 5.2 4.7 - - + -
203L VAL 3.5 1.2 - - - +
204L GLU* 3.3 4.0 - - - -
205L LYS* 3.2 31.6 + - + +
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Residues in contact with GLN 195 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146L THR 3.8 1.2 - - - +
148L ALA* 2.9 49.6 + - + +
149L TRP 6.3 1.1 - - - -
150L LYS* 5.9 9.3 - - + +
193L SER* 4.2 2.0 - - - +
194L CYS* 1.3 77.2 - - - +
196L VAL* 1.3 63.2 + - - +
197L THR* 4.9 2.3 - - - +
202L THR* 3.6 24.5 + - + +
203L VAL 3.0 8.3 - - - +
204L GLU* 3.7 27.4 - - + +
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Residues in contact with VAL 196 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114L PRO* 4.3 13.7 - - + +
116L VAL* 3.7 30.3 - - + -
135L CYS* 5.7 0.7 - - - -
137L ILE* 3.6 12.6 - - + -
145L VAL* 3.6 18.4 - - + -
146L THR 3.4 3.6 - - - -
147L VAL* 3.6 37.0 - - + -
194L CYS* 5.2 6.5 - - + -
195L GLN* 1.3 79.9 - - - +
197L THR* 1.3 60.6 + - - +
201L SER 3.8 0.9 - - - +
202L THR* 3.2 3.2 - - - -
203L VAL* 2.9 32.3 + - + +
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Residues in contact with THR 197 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144L ALA 3.9 1.4 - - - +
145L VAL* 3.5 10.1 - - - +
146L THR* 2.3 64.2 + - - +
148L ALA* 6.0 2.2 - - + -
195L GLN* 4.9 3.8 - - - +
196L VAL* 1.3 74.7 - - - +
198L HIS* 1.3 59.5 + - - +
199L GLU 4.2 0.6 + - - -
200L GLY* 4.1 12.2 + - - +
201L SER 3.3 5.4 - - - -
202L THR* 3.3 29.8 - - + +
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Residues in contact with HIS 198 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112L ALA 3.2 28.5 + - - -
113L ALA* 4.2 5.3 - - + +
114L PRO* 3.6 31.7 - - + +
140L PHE* 3.9 2.6 - + - +
141L TYR 3.3 15.3 + - - -
142L PRO* 2.7 27.8 + - + +
144L ALA 4.3 4.7 - - - -
145L VAL* 3.9 18.2 - - + -
197L THR* 1.3 74.4 - - - +
199L GLU* 1.3 102.4 + - - +
200L GLY 2.9 8.7 + - - +
201L SER* 2.7 28.5 + - - +
203L VAL* 6.1 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