Contacts of the strand formed by residues 50 - 59 (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 HIS 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ILE* 4.5 1.4 - - - +
40A CYS* 4.0 0.5 - - - -
46A ALA* 3.4 5.4 - - - +
47A TYR 3.0 28.0 + - - +
48A GLY 3.4 0.8 + - - -
49A SER* 1.3 91.4 + - - +
51A CYS* 1.3 65.5 + - - +
52A TYR* 3.5 24.1 + - + +
80A LEU* 6.5 0.4 - - + -
172A LYS* 3.6 34.2 - - + -
173A PHE 3.5 17.7 - - - +
174A THR* 3.9 9.6 - - + +
202A ZN 2.3 36.6 - - - -
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Residues in contact with CYS 51 (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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38A ILE* 5.1 2.0 - - - -
39A ARG 3.8 5.2 - - - -
40A CYS* 2.0 52.7 - - + -
41A PRO* 3.9 5.4 - - - -
44A SER* 4.0 0.7 - - - +
45A LYS 3.4 4.3 - - - -
49A SER 6.0 0.2 - - - -
50A HIS* 1.3 74.8 - - - +
52A TYR* 1.3 65.0 + - - +
172A LYS* 3.3 4.7 - - - -
173A PHE* 2.9 59.7 + - + +
175A ASP* 3.9 16.8 - - - -
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Residues in contact with TYR 52 (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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44A SER* 3.2 5.0 - - - -
45A LYS* 2.7 44.8 + - - +
47A TYR* 3.5 32.1 + + + -
50A HIS* 3.5 30.8 + - + +
51A CYS* 1.3 78.1 - - - +
53A ALA* 1.3 61.8 + - - +
77A VAL* 3.8 25.8 - - + -
84A GLU* 2.6 31.7 + - - -
87A PHE* 3.5 17.3 - + + -
88A VAL* 4.2 11.7 - - + -
91A LEU* 3.8 20.4 - - + +
170A VAL* 4.5 2.9 - - + -
171A CYS 3.2 6.1 - - - +
172A LYS* 3.7 18.2 - - + -
173A PHE* 4.4 0.4 - - - -
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Residues in contact with ALA 53 (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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43A GLY 4.1 9.4 - - - +
44A SER* 4.0 15.7 - - - +
52A TYR* 1.3 76.6 - - - +
54A LEU* 1.3 62.2 + - - +
55A PHE* 3.6 28.2 - - + -
91A LEU* 4.6 1.8 - - - -
170A VAL* 3.2 6.6 - - - -
171A CYS* 2.8 37.2 + - + +
173A PHE* 4.3 10.1 - - + -
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Residues in contact with LEU 54 (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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43A GLY 5.5 0.4 + - - -
53A ALA* 1.3 74.0 - - - +
55A PHE* 1.3 77.5 + - - +
56A LEU* 4.1 22.1 + - + +
91A LEU* 4.1 31.4 - - + +
92A VAL* 4.1 15.3 - - + -
94A SER* 6.1 0.4 - - - +
95A ILE* 4.2 25.8 - - + -
102A VAL* 4.3 5.2 - - + -
169A TYR 3.5 13.2 - - - +
170A VAL* 4.0 19.1 - - + -
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Residues in contact with PHE 55 (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* 3.6 34.1 - - + -
54A LEU* 1.3 75.3 - - - +
56A LEU* 1.3 63.5 + - - +
57A SER* 3.5 3.1 - - - +
70A LYS* 6.2 1.8 - - - -
71A ARG* 6.4 2.2 - - + -
168A PRO* 3.2 7.6 - - - +
169A TYR* 2.8 78.0 + + + +
171A CYS* 3.5 23.1 - - + -
173A PHE* 6.1 0.7 - + - -
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Residues in contact with LEU 56 (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* 4.1 18.6 - - + +
55A PHE* 1.3 73.0 - - - +
57A SER* 1.3 65.0 + - - +
58A PRO* 3.1 12.1 - - - +
95A ILE* 3.5 42.6 - - + +
99A TYR* 4.2 28.4 + - + +
168A PRO* 4.1 12.0 - - + +
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Residues in contact with SER 57 (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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55A PHE* 3.5 2.1 - - - +
56A LEU* 1.3 75.2 - - - +
58A PRO* 1.3 73.5 + - - +
59A LYS* 3.9 10.3 + - - +
169A TYR* 3.5 21.0 - - - -
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Residues in contact with PRO 58 (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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56A LEU 3.1 8.9 - - - +
57A SER* 1.3 88.7 + - - +
59A LYS* 1.3 65.7 + - - +
99A TYR* 5.7 4.0 - - + -
166A ARG* 3.6 41.3 - - + +
167A LEU* 3.3 15.7 - - - +
168A PRO* 4.0 3.6 - - + -
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Residues in contact with LYS 59 (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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57A SER* 3.6 11.4 + - - +
58A PRO* 1.3 79.2 - - - +
60A SER* 1.3 68.5 + - - +
63A ASP* 3.8 26.6 + - + +
64A ALA* 3.7 10.5 - - + +
67A ALA* 4.1 9.2 - - + -
70A LYS* 6.1 0.4 - - - +
103A TRP* 2.9 25.1 + - - -
166A ARG* 3.5 10.5 - - - +
167A LEU 2.9 11.6 + - - -
169A TYR* 3.4 31.6 - - + +
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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