Contacts of the strand formed by residues 173 - 181 (chain B) in PDB entry 4MT5
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 173 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B THR 3.0 14.3 + - - +
90B GLU* 3.3 16.4 - - + +
91B THR 2.9 27.6 + - - +
143B PHE* 4.8 8.7 - - + -
164B PHE* 3.8 44.0 - - + -
165B THR 5.8 0.4 - - - -
166B VAL* 3.9 24.5 - - + -
170B SER* 5.9 0.2 - - - +
171B LYS 4.1 7.0 - - - +
172B ASP* 1.3 77.5 - - - +
174B VAL* 1.3 66.9 + - - +
175B LYS* 4.5 18.4 - - + -
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Residues in contact with VAL 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B THR* 3.4 15.3 - - - +
93B HIS* 3.8 32.1 - - + +
172B ASP* 4.1 8.5 + - + -
173B ILE* 1.3 81.2 - - - +
175B LYS* 1.3 74.9 + - - +
176B THR* 4.7 3.4 - - - +
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Residues in contact with LYS 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B GLU* 6.3 0.2 - - + -
91B THR 3.2 5.9 + - - +
92B ILE* 3.5 14.7 - - + -
93B HIS* 2.9 24.5 + - - +
158B HIS* 6.0 5.2 - - + +
161B ILE* 4.2 35.7 - - + -
164B PHE* 3.6 32.3 - - + -
173B ILE* 4.5 15.3 - - + -
174B VAL* 1.3 84.7 - - - +
176B THR* 1.3 66.3 + - - +
177B VAL 4.2 0.4 - - - -
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Residues in contact with THR 176 (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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93B HIS* 3.5 25.3 - - + +
95B VAL* 3.9 27.1 - - + -
157B ASN* 4.5 2.4 + - - +
158B HIS* 4.3 12.4 + - - -
174B VAL* 4.7 3.5 - - - +
175B LYS* 1.3 80.0 + - - +
177B VAL* 1.3 64.4 + - - +
178B VAL* 3.9 11.5 + - + +
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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
----------------------------------------------------------
92B ILE* 4.0 22.0 - - + -
93B HIS 2.7 13.8 + - - +
94B TYR* 3.6 10.0 - - + -
95B VAL* 2.9 29.4 + - - +
148B SER* 4.0 6.7 - - - +
156B PRO* 3.9 15.0 - - + -
157B ASN* 3.7 10.8 - - - +
158B HIS* 3.9 22.9 - - + +
161B ILE* 4.1 14.4 - - + -
176B THR* 1.3 74.2 - - - +
178B VAL* 1.3 61.2 + - - +
179B TYR* 3.6 23.2 - - + -
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Residues in contact with VAL 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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95B VAL* 3.5 12.1 - - + +
96B ASP 3.4 28.7 - - - +
97B GLU* 4.4 5.4 - - - +
99B ASN* 5.6 1.8 - - - +
155B THR 4.1 0.2 - - - +
157B ASN* 2.9 45.5 + - + +
176B THR* 4.3 13.2 - - + +
177B VAL* 1.3 73.2 - - - +
179B TYR* 1.3 67.3 + - - +
180B VAL* 3.8 11.3 + - + +
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Residues in contact with TYR 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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94B TYR* 4.0 16.2 - + + -
95B VAL 2.7 23.9 + - - +
96B ASP* 3.5 20.4 - - + +
97B GLU* 3.5 10.7 + - - +
102B VAL* 4.2 10.5 - - + -
103B GLN* 3.5 7.7 + - - -
148B SER* 3.8 4.0 - - - -
149B PRO* 2.6 39.9 + - - +
151B VAL* 3.4 37.7 - - + -
154B TYR* 3.9 23.9 - - + -
155B THR 4.1 4.0 - - - -
156B PRO* 3.3 24.9 - - + -
177B VAL* 3.6 24.0 - - + -
178B VAL* 1.3 74.8 - - - +
180B VAL* 1.3 60.5 + - - +
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Residues in contact with VAL 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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97B GLU* 4.1 17.5 - - + +
154B TYR* 3.6 2.7 - - - -
155B THR* 3.0 33.1 + - - +
157B ASN* 6.4 1.1 - - + -
178B VAL* 3.8 13.6 + - + +
179B TYR* 1.3 75.0 - - - +
181B GLY* 1.3 77.6 + - - +
182B ASP* 3.3 3.8 + - - +
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Residues in contact with GLY 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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97B GLU* 3.0 21.6 + - - +
153B GLY 3.4 5.2 - - - -
154B TYR* 3.2 21.5 - - - -
180B VAL* 1.3 83.3 - - - +
182B ASP* 1.3 68.3 + - - +
183B PRO* 4.3 1.4 - - - +
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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