Contacts of the strand formed by residues 174 - 183 (chain L) in PDB entry 3LS5
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 174 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106L GLU* 2.7 46.9 + - - +
139L ASN 3.2 3.3 + - - -
140L PHE* 2.7 61.4 + - + +
141L TYR* 3.8 28.1 - + - -
143L LYS* 3.5 40.3 - - + +
164L TRP* 6.4 2.0 - - + -
165L THR* 4.1 13.7 - - - +
166L ASP* 5.2 0.2 - - - -
167L GLN* 3.5 38.1 + - + -
172L SER 4.1 0.2 - - - -
173L THR* 1.3 75.4 - - - +
175L SER* 1.3 62.8 + - - +
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Residues in contact with SER 175 (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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168H HIS* 3.3 27.6 + - - -
170H PHE* 3.5 10.8 - - - -
137L LEU 3.3 6.3 - - - -
138L ASN* 3.3 15.4 - - - -
139L ASN* 2.9 22.3 + - - -
140L PHE* 3.7 2.6 - - - -
164L TRP* 3.5 6.9 - - - +
165L THR* 3.1 37.2 + - - +
174L TYR* 1.3 71.5 + - - +
176L MET* 1.3 65.1 + - - +
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Residues in contact with MET 176 (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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170H PHE* 3.2 14.4 - - - -
136L PHE* 3.5 1.4 - - - -
137L LEU* 2.8 40.9 + - + +
140L PHE* 4.1 7.6 - - + -
145L ILE* 3.8 22.2 - - + +
146L ASN* 6.0 0.2 - - - -
147L VAL* 3.8 29.6 - - + +
162L ASN* 3.5 37.5 - - - +
163L SER 3.4 6.1 - - - +
164L TRP* 3.4 39.0 - - + +
175L SER* 1.3 80.3 - - - +
177L SER* 1.3 65.8 + - - +
178L SER* 4.7 0.7 - - - -
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Residues in contact with SER 177 (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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170H PHE* 3.7 22.0 - - - -
182H SER* 2.7 29.5 + - - -
134L VAL* 4.2 5.4 - - - +
135L CYS 3.5 4.7 + - - -
136L PHE* 3.4 10.6 - - - -
161L LEU 3.8 1.0 - - - +
162L ASN* 3.2 5.0 + - - -
163L SER* 2.9 35.7 + - - -
176L MET* 1.3 79.3 - - - +
178L SER* 1.3 62.2 + - - +
179L THR* 4.2 5.6 + - - -
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Residues in contact with SER 178 (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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134L VAL* 3.6 0.7 - - - +
135L CYS* 2.9 37.9 + - - -
137L LEU* 4.6 5.6 - - - -
147L VAL* 3.8 19.0 - - - +
149L TRP* 3.0 31.9 + - - -
160L VAL* 3.7 2.9 - - - +
161L LEU 3.5 0.4 - - - -
162L ASN* 2.5 26.5 + - - +
176L MET* 4.7 0.4 - - - -
177L SER* 1.3 75.3 + - - +
179L THR* 1.3 63.9 + - - +
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Residues in contact with THR 179 (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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145H LEU* 4.5 14.9 - - + +
147H LYS* 6.0 0.7 - - - -
180H THR* 5.3 8.1 - - + +
182H SER* 5.1 2.1 + - - -
132L SER* 3.9 15.5 - - - +
133L VAL 3.4 9.4 - - - +
134L VAL* 3.8 16.8 - - + +
149L TRP* 4.7 1.8 - - - -
159L GLY 3.4 2.8 - - - +
160L VAL* 3.3 3.7 - - - -
161L LEU* 2.8 46.5 + - - +
177L SER* 4.2 9.9 + - - -
178L SER* 1.3 77.1 + - - +
180L LEU* 1.3 61.8 + - - +
181L THR* 3.8 18.4 + - - +
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Residues in contact with LEU 180 (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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131L ALA 3.8 1.2 - - - +
132L SER* 3.2 1.0 - - - -
133L VAL* 2.7 43.3 + - + +
149L TRP* 3.9 42.5 - - + +
151L ILE* 4.1 20.4 - - + -
156L ARG* 3.8 15.0 - - + +
158L ASN 3.7 22.9 - - - +
159L GLY* 3.4 7.2 - - - +
160L VAL* 3.8 11.7 - - + +
179L THR* 1.3 72.0 - - - +
181L THR* 1.3 61.5 + - - +
182L LEU* 3.7 24.5 - - + +
193L TYR* 4.7 8.1 - - + -
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Residues in contact with THR 181 (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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147H LYS* 4.0 24.5 - - - +
125L GLN* 4.7 2.5 - - - +
130L GLY* 5.8 1.1 - - - -
131L ALA 3.5 4.3 - - - +
132L SER* 2.8 25.8 + - - +
156L ARG* 5.0 3.1 + - - -
159L GLY* 2.9 26.3 + - - +
179L THR* 3.8 10.4 + - - +
180L LEU* 1.3 76.6 - - - +
182L LEU* 1.3 75.3 + - - +
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Residues in contact with LEU 182 (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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130L GLY* 3.7 2.4 - - - -
131L ALA 2.8 35.9 + - - +
133L VAL* 5.6 2.0 - - + -
151L ILE* 4.1 14.6 - - + -
156L ARG* 4.4 9.0 - - - +
180L LEU* 3.7 37.5 - - + +
181L THR* 1.3 80.7 - - - +
183L THR* 1.3 61.9 + - - +
186L GLU* 3.8 24.0 - - + +
187L TYR* 3.3 46.0 - - + +
190L HIS* 5.9 0.2 - - + -
193L TYR* 4.2 13.7 - - + +
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Residues in contact with THR 183 (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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129L GLY 3.9 8.7 - - - +
130L GLY* 4.6 0.2 - - - -
131L ALA* 4.2 1.1 - - - -
182L LEU* 1.3 79.0 - - - +
184L LYS* 1.3 65.0 + - - +
185L ASP* 3.6 11.2 - - - +
186L GLU* 3.0 26.1 + - - +
187L TYR* 3.0 22.5 + - - +
189L ARG* 5.0 0.9 + - - -
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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