Contacts of the strand formed by residues 167 - 173 (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 LEU 167 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A PRO* 3.3 6.7 - - - +
59A LYS 2.9 26.0 + - - +
101A TYR* 3.8 40.2 - - + +
103A TRP* 3.5 42.1 - - + +
148A SER* 4.1 4.3 - - - -
161A TYR* 4.0 16.4 - - + +
165A VAL* 3.6 16.6 + - + -
166A ARG* 1.3 83.0 - - - +
168A PRO* 1.3 83.1 - - + +
169A TYR* 3.6 5.2 - - - -
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Residues in contact with PRO 168 (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* 4.5 1.8 - - + -
55A PHE 3.2 16.8 - - - +
56A LEU* 4.1 11.0 - - - +
58A PRO* 4.0 5.3 - - + -
95A ILE* 4.0 19.7 - - + -
99A TYR* 3.2 42.8 - - + -
101A TYR 3.5 12.8 - - - +
102A VAL* 3.4 5.9 - - + -
103A TRP* 2.9 20.6 + - - +
166A ARG 4.8 0.2 - - - +
167A LEU* 1.3 99.2 - - + +
169A TYR* 1.3 62.2 + - + +
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Residues in contact with TYR 169 (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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53A ALA 3.8 0.5 - - - +
54A LEU* 3.5 2.7 - - - +
55A PHE* 2.8 70.1 + + + +
57A SER 3.5 20.8 + - - -
59A LYS* 3.4 35.8 - - + -
64A ALA* 3.6 26.0 - - + -
67A ALA* 3.5 11.2 - - + +
68A CYS* 3.9 4.5 - - - -
70A LYS* 5.7 0.3 + - - -
76A LEU* 3.6 14.6 - - + -
102A VAL* 3.7 7.7 - - - +
103A TRP* 3.7 10.5 - - + -
167A LEU 3.6 14.4 - - - +
168A PRO* 1.3 75.5 - - - +
170A VAL* 1.3 64.2 + - - +
171A CYS* 3.7 21.5 - - - -
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Residues in contact with VAL 170 (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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52A TYR* 4.5 3.6 - - + -
53A ALA 3.2 9.0 - - - +
54A LEU* 4.0 9.4 - - + -
68A CYS* 4.4 0.7 - - - -
76A LEU* 3.5 9.0 - - - +
77A VAL* 2.8 50.0 + - + +
88A VAL* 4.7 9.2 - - + -
91A LEU* 3.9 19.3 - - + -
92A VAL* 3.5 31.6 - - + -
102A VAL* 3.9 9.4 - - + -
103A TRP 3.4 5.8 + - - +
104A ILE* 5.9 0.2 - - + -
149A LEU* 5.6 0.9 - - + -
169A TYR* 1.3 79.3 - - - +
171A CYS* 1.3 72.3 - - - +
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Residues in contact with CYS 171 (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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51A CYS 3.8 0.4 - - - +
52A TYR* 3.2 6.8 - - - +
53A ALA* 2.8 31.1 + - + +
55A PHE* 3.5 28.7 - - + -
67A ALA 4.8 0.7 - - - -
68A CYS* 2.0 57.4 - - + +
71A ARG* 6.1 2.5 - - + -
75A ASN 3.5 0.9 - - - +
77A VAL 4.4 0.2 - - - -
169A TYR* 3.7 10.1 - - - -
170A VAL* 1.3 78.3 - - - +
172A LYS* 1.3 60.1 + - - +
173A PHE* 4.3 13.0 - - + -
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Residues in contact with LYS 172 (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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50A HIS* 3.6 42.2 + - + -
51A CYS 3.3 4.3 - - - -
52A TYR* 3.7 15.3 - - + -
73A SER 3.8 2.8 - - - +
74A GLY* 3.4 0.9 - - - -
75A ASN* 2.9 30.4 + - + +
76A LEU 4.8 0.9 - - - +
77A VAL* 3.8 17.7 - - + +
78A SER* 3.0 38.7 + - - +
80A LEU* 3.9 12.7 - - - +
84A GLU* 2.7 34.3 + - - +
124A SER* 6.3 0.9 - - - -
126A ASP* 4.8 2.0 + - - -
171A CYS* 1.3 73.9 - - - +
173A PHE* 1.3 63.3 + - - +
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Residues in contact with PHE 173 (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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41A PRO* 3.8 16.2 - - + -
44A SER* 3.7 22.0 - - - -
50A HIS* 3.5 9.2 - - - -
51A CYS* 2.9 62.2 + - + -
52A TYR 4.2 0.9 - - - -
53A ALA* 4.3 14.6 - - + -
55A PHE* 6.3 0.2 - + - -
71A ARG* 3.2 55.2 - - + -
72A PRO 3.4 12.6 - - - +
73A SER 3.9 5.2 - - - -
74A GLY* 3.7 3.8 - - - -
171A CYS* 4.3 8.7 - - + -
172A LYS* 1.3 81.3 - - - +
174A THR* 1.3 83.0 + - - +
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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