Contacts of the strand formed by residues 110 - 117 (chain B) 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 SER 110 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B LYS* 2.9 12.2 + - - -
105B ILE* 4.6 4.3 - - - +
109B GLU* 1.3 78.2 - - - +
111B PHE* 1.3 66.9 + - - +
126B GLY* 6.3 0.2 - - - -
127B VAL 3.3 11.2 - - - -
128B ASN* 2.8 20.3 + - - +
150B VAL* 3.6 9.4 - - - +
288B THR* 3.6 7.1 - - - +
291B GLU* 2.7 33.9 + - - -
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Residues in contact with PHE 111 (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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105B ILE* 3.8 22.7 - - + -
109B GLU 4.2 2.7 - - - -
110B SER* 1.3 77.3 - - - +
112B ASN* 1.3 82.3 + - - +
113B ILE* 3.7 17.0 - - + -
126B GLY* 3.4 3.8 - - - -
127B VAL* 2.8 48.0 + - + +
129B MET* 4.0 17.5 - - + -
135B ILE* 3.8 23.8 - - + -
148B GLY* 3.9 0.4 - - - -
149B TYR 3.8 0.7 - - - +
150B VAL* 3.1 28.7 - - + -
159B VAL* 3.8 16.4 - - + -
160B TYR* 3.5 36.8 - + + -
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Residues in contact with ASN 112 (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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6B MET 4.4 1.6 - - - +
7B ALA* 3.1 12.2 - - + -
8B GLN* 2.7 57.0 + - - +
111B PHE* 1.3 80.0 - - - +
113B ILE* 1.3 61.9 + - - +
124B VAL* 4.8 0.2 - - + -
125B TYR 3.5 6.5 - - - +
126B GLY* 4.8 0.2 - - - -
147B VAL 3.9 0.2 - - - +
148B GLY* 2.9 26.9 - - - -
149B TYR* 2.9 57.7 + - + +
150B VAL* 3.9 1.4 - - - +
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Residues in contact with ILE 113 (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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111B PHE* 3.7 26.7 - - + -
112B ASN* 1.3 75.8 - - - +
114B LEU* 1.3 63.1 + - - +
115B ALA* 3.7 12.3 + - - +
123B SER 3.7 0.3 - - - +
124B VAL* 3.0 10.7 - - - +
125B TYR* 2.8 53.5 + - + +
127B VAL* 3.7 27.6 - - + -
135B ILE* 4.1 4.5 - - + -
139B PHE* 3.7 26.2 - - + -
146B SER* 4.6 1.6 - - - +
147B VAL 3.6 4.3 - - - +
148B GLY* 4.0 3.6 - - - -
149B TYR* 4.5 0.2 - - - -
160B TYR* 3.8 25.4 - - + -
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Residues in contact with LEU 114 (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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9A PRO* 4.2 10.8 - - + -
10B SER* 4.1 20.2 - - - +
13B VAL* 3.5 28.9 - - + -
14B GLU* 3.9 17.0 - - + +
17B ILE* 3.7 22.7 - - + -
113B ILE* 1.3 71.8 - - - +
115B ALA* 1.4 63.8 + - - +
116B CYS* 3.4 17.0 - - - -
121B PRO* 4.0 17.3 - - + -
123B SER 3.3 13.5 - - - +
124B VAL* 4.3 4.0 - - + +
146B SER* 3.4 13.5 - - - -
147B VAL* 2.9 20.2 + - + +
149B TYR* 4.1 14.5 - - + -
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Residues in contact with ALA 115 (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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6A MET* 5.3 0.7 - - - -
113B ILE* 3.7 5.3 - - + -
114B LEU* 1.4 72.0 - - - +
116B CYS* 1.3 53.9 + - - +
121B PRO* 3.8 0.7 - - - +
122B GLY* 2.8 30.0 + - - -
123B SER* 2.7 35.3 + - - +
125B TYR* 4.1 17.5 - - + +
138B SER 4.8 6.5 - - - +
139B PHE* 5.2 2.2 - - + -
143B THR* 5.2 9.2 - - + -
146B SER* 3.4 9.6 - - - +
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Residues in contact with CYS 116 (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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17B ILE* 3.5 39.0 - - + -
28B ASN* 3.0 37.8 + - + +
114B LEU* 3.4 20.9 - - - -
115B ALA* 1.3 75.8 - - - +
117B TYR* 1.3 59.9 + - - +
120B CYS 3.4 8.7 - - - +
121B PRO* 3.7 13.2 - - - -
122B GLY* 5.7 0.4 - - - -
143B THR* 3.2 19.8 - - - +
146B SER* 2.9 12.1 + - - +
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Residues in contact with TYR 117 (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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299A VAL 4.3 19.9 + - - -
116B CYS* 1.3 73.1 - - - +
118B GLU* 1.3 103.7 + - + +
119B GLY 3.2 0.2 - - - -
120B CYS* 3.0 26.8 + - + +
122B GLY* 4.9 2.6 - - - +
140B ILE* 5.2 7.0 - - + -
141B ALA 3.6 23.6 - - - -
142B GLY* 3.9 14.1 - - - -
143B THR* 4.8 6.7 - - + -
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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