Contacts of the strand formed by residues 101 - 107 (chain A) in PDB entry 4MTH
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 TYR 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A TYR* 3.7 1.6 - - - +
100A SER* 1.3 105.1 + - - +
102A VAL* 1.3 65.9 + - - +
134A GLU* 5.4 0.2 - - - -
148A SER* 3.6 18.8 - - - +
149A LEU 3.2 9.9 - - - +
150A SER* 3.6 23.9 - - - -
152A SER* 5.2 5.0 + - - -
155A PHE* 4.6 0.2 - - - -
159A LYS* 4.1 15.1 - - + +
161A TYR* 3.5 34.1 - + + -
167A LEU* 3.8 29.2 - - + +
168A PRO* 3.5 22.7 - - - +
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Residues in contact with VAL 102 (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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54A LEU* 4.3 4.0 - - + -
92A VAL* 4.5 9.9 - - + -
95A ILE* 4.0 23.8 - - + -
99A TYR* 5.5 0.7 - - + -
101A TYR* 1.3 82.0 - - - +
103A TRP* 1.3 70.7 + - - +
104A ILE* 4.2 0.5 - - - +
148A SER* 3.1 4.1 - - - -
149A LEU* 2.8 46.3 + - + +
155A PHE* 4.0 21.8 - - + -
167A LEU* 4.5 0.2 - - - -
168A PRO* 3.4 12.8 - - + +
169A TYR* 3.7 16.2 - - - +
170A VAL* 3.9 19.1 - - + -
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Residues in contact with TRP 103 (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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59A LYS 2.9 29.4 + - - -
60A SER 4.1 1.1 - - - -
61A TRP* 3.4 25.7 - + + +
64A ALA* 4.3 5.4 - - + -
76A LEU* 4.0 11.4 - - + +
102A VAL* 1.3 73.3 - - - +
104A ILE* 1.3 65.3 + - - +
146A CYS* 3.4 28.0 - - + -
147A ALA 3.2 26.7 - - - -
148A SER* 4.1 1.8 - - - -
161A TYR* 3.8 24.5 - + + -
162A ASN 3.3 26.5 - - - -
163A CYS 3.8 8.1 - - - -
165A VAL 3.2 20.6 + - - -
167A LEU* 3.5 32.5 - - + +
168A PRO 2.9 10.5 + - - -
169A TYR* 3.7 11.8 - - + +
170A VAL* 3.4 22.9 + - - +
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Residues in contact with ILE 104 (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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61A TRP* 2.9 23.0 + - - -
76A LEU* 3.7 6.5 - - - +
77A VAL* 3.5 29.8 - - + +
79A VAL* 4.5 5.2 - - + -
102A VAL* 3.5 1.1 + - + +
103A TRP* 1.3 76.7 - - - +
105A GLY* 1.3 60.4 + - - +
106A LEU 3.1 5.5 + - - +
122A TRP* 3.9 20.6 - - + -
147A ALA* 3.2 29.0 + - + +
148A SER 4.6 1.3 - - - +
149A LEU* 3.5 32.8 - - + -
158A TRP* 3.6 40.6 - - + +
170A VAL* 5.6 0.2 - - + -
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Residues in contact with GLY 105 (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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61A TRP* 3.6 9.5 - - - -
76A LEU* 3.3 23.6 - - - +
77A VAL 2.8 20.1 + - - -
104A ILE* 1.3 71.4 - - - +
106A LEU* 1.3 58.4 + - - +
121A GLU 3.5 0.7 - - - +
122A TRP* 3.4 9.1 - - - -
123A SER* 2.9 36.1 + - - -
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Residues in contact with LEU 106 (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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61A TRP* 3.6 4.4 + - - -
104A ILE* 3.1 4.9 + - + -
105A GLY* 1.3 76.8 - - - +
107A HIS* 1.3 65.3 + - - +
120A TRP* 3.9 9.2 - - + -
121A GLU 3.6 16.2 - - - +
122A TRP* 3.4 40.8 - - + -
128A MET* 3.5 29.4 - - + -
133A TRP* 3.5 36.3 - - + -
146A CYS* 3.5 0.9 - - - -
147A ALA* 2.9 36.5 + - + -
158A TRP* 4.0 13.9 - - + -
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Residues in contact with HIS 107 (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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61A TRP* 3.4 42.7 - + + -
105A GLY 4.9 0.7 - - - -
106A LEU* 1.3 76.2 - - - +
108A ASP* 1.3 60.9 + - - +
109A PRO* 3.5 20.8 - - + +
120A TRP* 3.2 8.8 - - - -
121A GLU* 2.8 43.4 + - + -
123A SER 5.1 2.0 - - - -
145A HIS 3.3 12.1 - - - +
146A CYS* 3.9 7.3 - - - -
163A CYS* 5.2 0.2 - - - -
201A ZN 2.0 38.1 - - - -
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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