Contacts of the strand formed by residues 173 - 181 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A VAL* 5.4 0.4 - - + -
89A THR 2.8 12.3 + - - +
90A GLU* 3.3 27.2 - - + +
91A THR* 2.7 33.6 + - - +
143A PHE* 4.4 10.5 - - + -
164A PHE* 3.7 43.1 - - + -
166A VAL* 4.2 19.3 - - + -
171A LYS 4.0 7.2 - - - +
172A ASP* 1.3 76.2 - - - +
174A VAL* 1.3 63.7 + - - +
175A LYS* 4.5 18.4 - - + +
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Residues in contact with VAL 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A THR* 3.6 9.9 - - - +
93A HIS* 4.0 29.2 - - + +
172A ASP* 3.9 12.2 + - + +
173A ILE* 1.3 80.2 - - - +
175A LYS* 1.3 74.0 + - - +
176A THR* 5.2 2.2 - - - +
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Residues in contact with LYS 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A THR 3.0 5.9 + - - +
92A ILE* 3.2 28.8 - - + +
93A HIS* 3.0 22.3 + - - +
158A HIS* 6.5 0.9 - - + -
161A ILE* 3.8 27.8 - - + -
164A PHE* 3.9 29.0 - - + -
173A ILE* 4.5 12.5 - - + +
174A VAL* 1.3 85.1 + - - +
176A THR* 1.3 63.7 + - - +
177A VAL* 5.4 1.1 - - + -
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Residues in contact with THR 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A HIS* 3.5 29.8 - - + +
95A VAL* 3.9 25.8 - - + -
99A ASN* 5.8 2.0 - - - +
157A ASN* 4.8 1.0 + - - +
158A HIS* 4.5 13.0 - - - -
174A VAL* 5.2 2.6 - - - +
175A LYS* 1.3 77.2 + - - +
177A VAL* 1.3 65.2 + - - +
178A VAL* 4.1 9.7 + - + +
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Residues in contact with VAL 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ILE* 3.6 28.0 - - + -
93A HIS 2.5 12.5 + - - +
94A TYR* 3.4 16.4 - - + -
95A VAL* 2.8 32.7 + - - +
148A SER* 3.8 20.4 - - - +
156A PRO* 3.8 22.2 - - + -
157A ASN* 3.9 7.9 - - - +
158A HIS* 3.9 14.1 - - + +
160A GLN 6.4 0.2 - - - -
161A ILE* 5.7 7.6 - - + +
175A LYS* 5.4 0.9 - - + -
176A THR* 1.3 75.5 - - - +
178A VAL* 1.3 59.7 + - - +
179A TYR* 4.2 7.8 - - + -
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Residues in contact with VAL 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A VAL* 3.8 15.3 - - + -
96A ASP 3.4 28.3 - - - +
97A GLU* 4.4 9.4 - - - +
156A PRO* 3.4 0.3 - - - +
157A ASN* 3.0 52.6 + - - +
176A THR* 4.5 9.9 - - + +
177A VAL* 1.3 75.7 - - - +
179A TYR* 1.3 69.6 + - - +
180A VAL* 3.8 6.5 + - + +
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Residues in contact with TYR 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A TYR* 3.9 26.5 - + + -
95A VAL 3.0 14.1 + - - +
96A ASP* 3.6 20.0 - - - +
97A GLU* 4.0 5.7 - - - +
102A VAL* 3.6 22.2 - - + -
103A GLN* 4.9 0.9 - - + -
148A SER* 3.7 4.9 - - - -
149A PRO* 2.3 45.2 + - - +
151A VAL* 3.5 28.8 - - + +
154A TYR* 3.7 30.6 - + + -
155A THR 4.0 2.2 - - - -
156A PRO* 3.5 37.5 - - + -
177A VAL* 4.2 7.4 - - + -
178A VAL* 1.3 78.6 - - - +
180A VAL* 1.3 62.3 + - - +
181A GLY 3.9 1.2 + - - -
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Residues in contact with VAL 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A GLU* 3.4 21.5 - - - +
154A TYR* 3.2 3.5 - - - -
155A THR* 3.0 42.9 + - - +
157A ASN* 5.6 7.6 - - + +
178A VAL* 4.7 9.0 - - + +
179A TYR* 1.3 74.0 - - - +
181A GLY* 1.3 76.0 + - - +
182A ASP* 3.6 1.6 + - - +
183A PRO* 5.5 4.9 - - + -
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Residues in contact with GLY 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A GLU* 4.1 6.9 + - - +
153A GLY 3.6 1.3 - - - -
154A TYR* 3.5 24.3 - - - -
179A TYR 3.9 1.0 + - - -
180A VAL* 1.3 85.6 - - - +
182A ASP* 1.3 64.2 + - - -
183A PRO* 3.2 12.0 - - - +
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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