Contacts of the strand formed by residues 149 - 154 (chain B) in PDB entry 4TLG
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 ALA 149 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96B CYS* 4.4 2.0 - - - -
97B PRO* 3.3 20.4 - - + +
131B LEU* 3.9 37.0 - - + -
135B CYS* 4.3 1.7 - - - -
148B MET* 1.3 72.6 - - - +
150B LEU* 1.3 62.0 + - - +
185B THR 2.9 10.8 + - - +
186B LEU* 3.4 11.6 - - + -
187B LYS* 2.8 28.8 + - - +
505B EDO 4.3 3.6 - - - -
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Residues in contact with LEU 150 (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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92B ASP* 3.8 34.3 - - + +
96B CYS* 4.7 0.6 - - + +
97B PRO 2.9 10.7 + - - +
98B VAL* 3.3 8.3 - - + +
99B TYR* 2.9 24.9 + - - +
149B ALA* 1.3 74.5 - - - +
151B MET* 1.3 63.5 + - - +
152B VAL* 5.2 1.3 - - + -
187B LYS* 4.7 8.3 - - + -
188B ASN* 3.3 44.6 - - + +
190B ILE* 3.9 16.2 - - + -
231B PHE* 4.1 14.8 - - + -
232B ILE* 3.8 26.0 - - + -
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Residues in contact with MET 151 (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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99B TYR* 3.3 31.0 - - + +
101B ASN* 5.5 3.1 - - + -
127B VAL* 4.6 7.2 - - + -
128B CYS* 5.2 1.6 - - - -
131B LEU* 4.1 22.7 - - + -
149B ALA 4.3 0.4 + - - -
150B LEU* 1.3 74.9 - - - +
152B VAL* 1.3 58.7 + - - +
153B PHE* 3.8 33.5 - - + -
174B PHE* 4.5 22.9 - - + -
175B PHE* 6.5 0.2 - - - -
178B LEU* 5.5 0.2 - - + -
186B LEU* 4.0 32.9 - - + +
188B ASN 3.1 12.4 + - - +
189B LEU* 3.5 2.3 - - - -
190B ILE* 2.8 33.8 + - - +
505B EDO 4.3 7.2 - - - +
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Residues in contact with VAL 152 (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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98B VAL* 4.1 21.1 - - + -
99B TYR 2.8 7.2 + - - +
100B PHE* 3.5 31.3 - - + -
101B ASN* 2.7 34.5 + - - +
150B LEU* 5.2 1.3 - - + -
151B MET* 1.3 76.4 - - - +
153B PHE* 1.3 61.3 + - - +
154B ASP 4.7 0.7 - - - +
190B ILE* 3.3 16.2 - - + +
192B ILE* 3.9 31.6 - - + -
228B LEU* 4.3 20.0 - - + -
232B ILE* 4.4 7.0 - - + -
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Residues in contact with PHE 153 (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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101B ASN* 3.5 36.1 - - + +
103B ILE* 4.3 9.4 - - + -
151B MET* 3.8 39.0 - - + -
152B VAL* 1.3 72.9 - - - +
154B ASP* 1.3 61.4 + - - +
155B MET* 3.6 16.6 + - - +
171B TYR* 5.2 3.8 - + - -
174B PHE* 5.7 2.2 - + - -
175B PHE* 4.5 14.4 - + - -
186B LEU* 5.8 0.2 - - + -
189B LEU* 3.8 31.9 - - + -
190B ILE 2.7 17.8 + - - +
191B VAL* 3.5 7.9 - - + -
192B ILE* 2.9 31.5 + - - +
510B 11A 4.0 28.5 - - + -
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Residues in contact with ASP 154 (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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100B PHE* 5.9 0.2 - - + -
101B ASN 2.8 15.4 + - - +
102B ILE* 3.8 27.5 - - + +
103B ILE* 3.2 9.0 + - - +
104B GLY 3.1 21.0 + - - -
152B VAL* 4.0 2.5 - - + -
153B PHE* 1.3 70.5 - - - +
155B MET* 1.3 64.0 + - - +
156B GLU* 3.2 12.4 + - - +
192B ILE* 3.7 14.1 - - + +
193B ARG* 2.8 48.8 + - - +
241B PHE* 3.7 10.4 - - + -
260B TYR* 5.5 1.0 - - - -
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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