Contacts of the strand formed by residues 155 - 165 (chain F) in PDB entry 1LVO
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 ILE 155 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99F GLU 6.4 0.2 - - - -
100F HIS* 5.4 1.3 - - - -
101F LYS* 3.9 29.2 - - + +
151F LEU* 3.4 5.7 - - - +
152F GLU 3.1 27.7 + - - +
153F ASN* 3.1 15.9 - - + +
154F GLY* 1.3 80.5 - - - +
156F LEU* 1.3 64.2 + - - +
157F TYR* 3.3 44.4 - - + +
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Residues in contact with LEU 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F LEU* 4.0 19.5 - - + -
13F VAL* 4.2 7.2 - - + -
98F PRO* 3.5 35.7 - - + -
99F GLU 3.7 15.5 + - - +
100F HIS* 3.2 5.7 - - + +
101F LYS* 2.9 24.8 + - - -
149F TYR* 4.0 29.8 - - + -
150F VAL 3.8 2.0 - - - +
151F LEU* 3.6 25.4 - - + -
154F GLY 4.0 2.0 + - - -
155F ILE* 1.3 73.1 - - - +
157F TYR* 1.3 65.1 + - - +
158F PHE* 3.7 21.8 - - + -
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Residues in contact with TYR 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101F LYS* 3.3 35.7 - - + +
102F PHE 5.4 0.4 - - - -
103F LYS* 3.2 39.3 - - + -
149F TYR* 3.0 8.9 - - - +
150F VAL* 2.9 53.7 + - + -
152F GLU* 3.2 33.9 + - + +
155F ILE* 3.3 50.2 - - + +
156F LEU* 1.3 74.3 - - - +
158F PHE* 1.3 63.2 + - - +
159F VAL* 3.6 1.1 + - + +
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Residues in contact with PHE 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F VAL* 3.9 32.8 - - + -
16F CYS* 4.7 4.0 - - - -
30F LEU* 4.0 14.4 - - + -
32F LEU* 3.7 34.1 - - + -
98F PRO* 4.5 4.9 - - + -
100F HIS* 3.7 38.8 - + + -
101F LYS 3.0 5.5 + - - -
102F PHE* 3.6 25.2 - + + +
103F LYS 3.5 18.5 + - - +
147F VAL* 3.8 20.4 - - + -
148F GLY 3.9 0.9 - - - -
149F TYR* 4.3 5.6 - - + -
156F LEU* 3.7 20.0 - - + -
157F TYR* 1.3 73.8 - - - +
159F VAL* 1.3 58.0 + - - +
176F PHE* 3.6 12.9 - - + -
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Residues in contact with VAL 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F LYS* 3.3 38.1 - - + +
105F ILE* 3.5 32.3 - - + -
111F PHE* 3.8 22.9 - - + -
148F GLY 2.9 20.7 + - - +
149F TYR* 4.2 1.8 - - - +
150F VAL* 4.0 10.1 - - + -
157F TYR 3.9 9.2 - - - +
158F PHE* 1.3 76.2 - - - +
160F TYR* 1.3 59.9 + - + +
174F SER 4.3 0.2 - - - -
175F ASN* 3.7 6.4 - - - +
176F PHE* 4.1 7.2 - - - +
181F TYR* 2.7 30.1 + - - +
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Residues in contact with TYR 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111F PHE* 3.5 29.8 - + + -
113F ILE* 4.0 12.6 - - + -
129F MET* 5.1 2.7 - - + -
134F THR* 6.3 0.9 - - - -
135F ILE* 3.6 31.3 - - + +
139F PHE* 4.0 6.5 - + - -
146F SER 4.4 1.3 - - - -
147F VAL* 3.3 4.9 - - - -
148F GLY* 2.6 33.6 + - - +
159F VAL* 1.3 81.7 - - + +
161F MET* 1.3 62.2 + - - +
162F HIS* 2.8 45.6 + - + -
171F HIS 3.8 5.7 - - - -
172F VAL 3.3 10.6 - - - -
173F GLY* 3.3 24.5 - - - -
174F SER 3.3 4.7 - - - -
176F PHE* 3.7 9.5 - - - -
181F TYR* 3.9 21.8 - + + -
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Residues in contact with MET 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F ASN 4.6 0.7 - - - +
30F LEU* 4.1 13.2 - - + +
37F ILE* 3.2 34.1 - - - +
38F CYS* 3.6 29.8 - - - -
39F PRO* 3.9 4.9 - - + -
85F ASN* 4.8 6.5 - - - +
145F GLY* 3.7 28.5 - - - +
146F SER 3.4 2.9 - - - -
147F VAL* 4.3 3.4 - - + -
160F TYR* 1.3 77.0 - - - +
162F HIS* 1.3 66.1 + - - +
163F HIS* 3.3 4.9 - - + -
173F GLY* 3.1 2.8 - - - -
174F SER* 3.0 39.3 + - - +
175F ASN 5.6 0.2 - - - +
176F PHE* 3.9 24.9 - - + -
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Residues in contact with HIS 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F PRO* 3.4 9.9 - - - +
139F PHE* 3.4 56.2 - + + +
143F THR* 4.2 1.1 - - - -
144F CYS* 3.6 20.7 - - - -
145F GLY 2.7 25.3 + - - -
146F SER 2.9 22.1 + - - +
160F TYR* 2.8 34.2 + - + -
161F MET* 1.3 72.0 - - - +
163F HIS* 1.3 58.8 - - - +
164F LEU* 3.2 36.6 + - - -
165F GLU* 4.7 0.6 + - - +
171F HIS* 3.7 9.4 - + + -
172F VAL 3.3 6.1 + - - -
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Residues in contact with HIS 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F PRO* 3.9 23.0 - - + +
40F ARG 4.5 0.4 - - - -
41F HIS* 2.9 35.2 + - + +
84F VAL* 3.1 39.7 - - + -
85F ASN* 3.5 4.8 + - - -
144F CYS* 4.0 8.5 - - - -
161F MET* 3.3 22.4 - - - +
162F HIS* 1.3 80.8 - - - +
164F LEU* 1.3 78.9 + - + +
172F VAL 3.0 11.6 + - - +
174F SER* 2.8 34.9 + - - -
180F MET* 3.6 14.5 - - + +
186F ASP* 4.4 5.2 - - - +
4006F MRD 4.0 2.4 + - - -
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Residues in contact with LEU 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F CYS* 5.6 1.3 - - - -
162F HIS* 3.2 14.7 - - - -
163F HIS* 1.3 92.8 - - + +
165F GLU* 1.3 74.3 + - - +
166F LEU* 4.0 10.3 - - + -
172F VAL* 2.8 72.2 + - + -
180F MET* 3.7 11.4 - - + -
185F GLU 4.6 9.9 - - - +
186F ASP* 4.9 2.9 - - + -
187F GLN 5.7 3.6 - - - +
191F GLN* 4.7 7.9 - - - +
4006F MRD 3.8 26.5 - - + +
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Residues in contact with GLU 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E SER* 5.4 5.4 - - - -
139F PHE 3.9 10.7 - - - +
162F HIS* 5.4 0.9 - - - +
164F LEU* 1.3 84.9 - - - +
166F LEU* 1.3 70.1 + - - +
167F GLY 5.4 0.5 - - - +
169F GLY* 3.7 19.7 - - - -
170F SER 3.4 5.2 - - - +
171F HIS* 2.9 35.2 + - + -
4006F MRD 6.2 0.8 - - - +
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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