Contacts of the strand formed by residues 174 - 185 (chain B) in PDB entry 5LAL
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B HIS* 2.7 40.3 + - + -
49B ASP 3.2 16.2 - - - -
50B ILE* 3.7 15.0 - - + -
90B LYS 4.1 0.2 + - - -
92B TYR* 4.2 11.1 - + + +
168B LEU* 3.9 13.7 - - + -
169B PHE* 3.7 3.2 - - - -
170B GLN* 2.8 60.8 + - + +
171B GLY 4.6 0.2 - - - +
172B ALA 3.8 0.8 - - - -
173B LYS* 1.3 81.0 - - + +
175B PHE* 1.3 73.1 + - - +
176B ARG* 2.8 39.7 + - + +
1E NAG 3.8 16.6 - - - +
2E NAG 3.6 20.1 - - + +
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Residues in contact with PHE 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B PHE* 3.8 24.0 - + - -
48B HIS* 3.6 2.4 - - - -
49B ASP* 2.9 54.4 + - + +
51B LEU* 6.5 0.2 - - + -
104B TYR* 3.5 36.1 - + - -
106B TYR* 4.8 1.6 - - - -
116B PHE* 4.4 4.7 - + - -
168B LEU 3.2 12.3 - - - +
169B PHE* 3.8 33.2 - + + -
174B TYR* 1.3 85.0 - - - +
176B ARG* 1.3 62.9 + - - +
177B VAL* 3.8 20.9 - - + -
218B GLY* 3.6 27.6 - - - -
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Residues in contact with ARG 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B TYR* 4.1 16.2 - - + -
47B PHE 3.2 10.5 - - - +
48B HIS* 4.0 9.0 - - + +
90B LYS* 3.2 46.3 + - - +
92B TYR* 6.0 0.2 - - - -
166B THR* 3.9 1.9 - - - +
167B ASP* 2.9 53.4 + - + -
168B LEU* 2.8 44.2 + - - +
174B TYR* 2.8 34.8 + - + +
175B PHE* 1.3 73.2 - - - +
177B VAL* 1.3 66.0 + - - +
2E NAG 3.9 11.9 - - - +
5E MAN 4.9 1.6 + - - -
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Residues in contact with VAL 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B TYR* 3.3 6.9 - - - -
47B PHE* 2.9 44.0 + - + +
144B ARG* 4.8 2.2 - - - +
164B PHE* 3.7 34.8 - - + -
165B VAL 3.6 10.1 - - - +
166B THR* 4.8 8.1 - - + +
169B PHE* 6.2 0.2 - - + -
175B PHE* 3.8 26.5 - - + -
176B ARG* 1.3 77.1 - - - +
178B LYS* 1.3 76.9 + - - +
179B MET* 3.5 9.3 + - + -
218B GLY* 4.4 13.7 - - - +
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Residues in contact with LYS 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B SER* 3.2 23.3 - - - +
45B PHE 3.5 6.7 - - - +
46B TYR* 3.8 25.2 - - + +
163B THR 3.4 4.9 - - - +
165B VAL* 2.8 46.2 + - + +
167B ASP* 4.5 1.4 - - - +
176B ARG 4.3 0.8 + - - -
177B VAL* 1.3 72.4 - - - +
179B MET* 1.3 60.0 + - - +
180B ASP* 3.5 20.9 + - - +
215B EDO 3.7 30.7 - - - +
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Residues in contact with MET 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B PHE 3.8 0.5 - - - +
44B SER* 3.4 1.7 - - - -
45B PHE* 2.8 50.9 + - + +
47B PHE* 3.5 45.5 - - + -
82B PHE* 6.2 0.4 - - + -
86B ILE* 4.1 13.5 - - + -
116B PHE* 5.4 1.6 - - + -
118B TYR* 3.3 43.1 - - + +
120B LEU* 4.5 6.7 - - - -
163B THR 3.4 4.9 - - - +
164B PHE* 3.7 26.9 - - + -
177B VAL* 3.5 6.9 + - + -
178B LYS* 1.3 71.9 - - - +
180B ASP* 1.3 63.9 + - - +
181B ILE* 4.0 7.4 - - + -
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Residues in contact with ASP 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B HIS* 4.0 17.4 - - - +
43B PHE 3.3 3.8 - - - -
44B SER* 2.4 31.2 + - - -
161B ILE 3.6 1.6 - - - +
162B ALA* 3.4 2.4 - - - -
163B THR* 2.8 57.7 + - - +
165B VAL* 5.4 4.7 - - - +
178B LYS* 3.5 22.5 + - - +
179B MET* 1.3 72.5 - - - +
181B ILE* 1.3 63.0 + - - +
182B LYS* 3.8 10.1 + - - +
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Residues in contact with ILE 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LYS 3.7 1.4 - - - +
42B HIS* 3.2 6.9 - - - -
43B PHE* 2.7 49.3 + - + +
45B PHE* 3.9 30.1 - - + -
118B TYR* 5.1 1.1 - - - +
120B LEU* 4.0 8.5 - - + -
131B LEU* 3.9 15.9 - - + -
133B ILE* 3.9 17.9 - - + -
148B VAL* 4.4 5.8 - - + -
161B ILE 3.7 0.9 - - - -
162B ALA* 3.7 26.7 - - + -
179B MET* 4.7 8.1 - - + -
180B ASP* 1.3 73.0 - - - +
182B LYS* 1.3 62.0 + - - +
183B LEU* 3.7 27.8 - - + -
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Residues in contact with LYS 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B PRO* 3.9 12.3 - - + -
41B LYS 3.5 4.5 - - - -
42B HIS* 3.9 22.0 - - + -
145B ASP* 4.7 2.4 + - - -
160B GLY* 3.2 2.8 - - - -
161B ILE* 2.8 49.8 + - + +
163B THR* 2.7 32.9 + - - +
180B ASP* 4.3 17.7 - - - +
181B ILE* 1.3 76.9 - - - +
183B LEU* 1.3 63.0 + - - +
184B TYR* 3.4 29.9 + - + +
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Residues in contact with LEU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B PRO* 3.3 3.6 - - - +
40B CYS* 2.8 32.8 + - - -
41B LYS* 2.8 32.9 + - + +
43B PHE* 5.6 0.9 - - + -
131B LEU* 4.3 7.2 - - + -
148B VAL* 3.9 26.7 - - + -
155B PHE* 4.0 29.2 - - + -
158B ALA* 4.3 12.3 - - + -
159B ARG 3.6 9.2 - - - +
181B ILE* 3.7 24.9 - - + -
182B LYS* 1.3 76.1 - - - +
184B TYR* 1.3 54.7 + - - +
185B GLU 3.6 3.6 - - - +
186B CYS* 3.9 15.5 - - - -
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Residues in contact with TYR 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ILE* 3.3 4.7 - - - +
35B ASP 3.0 48.3 + - - +
36B GLN* 4.5 8.7 - - - -
37B LYS 5.0 0.4 - - - -
38B LYS* 3.4 16.6 - - - -
39B PRO* 3.4 24.4 - - + +
40B CYS* 3.6 7.4 - - - +
159B ARG 2.9 7.2 + - - +
160B GLY* 4.0 9.2 - - - -
161B ILE* 4.0 17.8 - - + +
182B LYS* 3.4 46.3 + - + +
183B LEU* 1.3 73.7 - - - +
185B GLU* 1.3 58.7 + - - +
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Residues in contact with GLU 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B THR 3.2 4.3 - - - -
34B ILE* 3.7 16.5 - - + +
157B MET* 4.0 14.7 - - - +
158B ALA* 3.6 10.0 - - - +
159B ARG* 2.8 67.5 + - + +
183B LEU* 4.2 1.9 - - - +
184B TYR* 1.3 76.9 - - - +
186B CYS* 1.3 63.3 + - - +
187B TYR* 2.4 45.7 + - + +
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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