Contacts of the strand formed by residues 128 - 139 (chain A) in PDB entry 4Z4H
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 PHE 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A ILE* 3.8 10.5 - - + -
62A LYS 3.7 4.7 - - - -
63A PRO* 3.6 27.8 - - + -
66A CYS* 3.5 31.6 - - - -
70A VAL* 4.5 5.2 - - + -
74A ILE* 3.6 34.5 - - + -
116A GLU* 3.5 7.8 - - - +
117A VAL* 2.9 50.1 + - + +
119A LEU* 4.6 18.6 - - + -
127A ILE* 1.3 88.6 - - + +
129A LYS* 1.3 63.8 + - - +
17B C 5.5 2.5 - - - -
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Residues in contact with LYS 129 (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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60A ASP 3.4 3.6 - - - +
61A ILE* 3.5 1.6 - - - -
62A LYS* 3.0 47.3 + - + +
114A GLU* 3.4 26.9 - - + +
115A LEU 3.3 5.4 - - - +
116A GLU* 3.4 31.2 + - + -
128A PHE* 1.3 78.6 - - - +
130A VAL* 1.3 61.1 - - - +
131A SER 4.1 0.2 + - - -
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Residues in contact with VAL 130 (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 LEU* 4.7 7.9 - - + -
60A ASP 3.2 7.4 - - - +
61A ILE* 4.1 16.8 - - + -
74A ILE* 3.6 29.8 - - + -
75A VAL* 5.5 0.2 - - + -
78A MET* 4.0 24.9 - - + -
113A VAL 3.3 3.5 - - - +
114A GLU* 4.3 2.0 - - - -
115A LEU* 2.6 47.0 + - + +
117A VAL* 4.1 16.6 - - + -
129A LYS* 1.3 75.9 - - - +
131A SER* 1.3 68.4 + - - +
132A ILE* 4.2 8.1 - - + -
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Residues in contact with SER 131 (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 LEU* 3.3 5.7 - - - -
60A ASP* 2.9 55.2 + - - +
112A LYS* 4.3 22.6 + - - -
113A VAL 3.5 6.1 - - - -
114A GLU* 3.4 19.6 + - - -
129A LYS 4.1 0.8 + - - -
130A VAL* 1.3 74.1 - - - +
132A ILE* 1.3 62.9 + - - +
133A LYS* 4.2 5.2 - - - +
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Residues in contact with ILE 132 (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 TYR* 4.3 18.6 - - + -
58A GLU 3.5 8.1 - - - +
59A LEU* 4.3 11.4 - - + -
78A MET* 4.2 13.0 - - + -
86A ILE* 5.8 1.1 - - + -
87A PHE* 4.2 21.5 - - + -
100A LEU* 5.4 3.4 - - + -
106A LEU* 5.2 2.9 - - + -
108A ILE* 4.4 19.7 - - + +
111A ASP 3.6 5.0 - - - +
112A LYS* 3.5 5.4 - - - -
113A VAL* 3.3 36.7 + - + +
115A LEU* 4.0 23.6 - - + -
130A VAL* 4.2 9.9 - - + +
131A SER* 1.3 80.2 - - - +
133A LYS* 1.3 63.4 + - - +
134A TRP 4.2 0.3 + - - -
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Residues in contact with LYS 133 (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 TYR* 3.5 3.9 - - - -
58A GLU* 2.6 58.5 + - + +
110A ARG 5.0 6.7 - - - +
111A ASP 4.8 2.5 - - - -
112A LYS* 3.5 52.4 - - + +
131A SER* 4.2 5.3 - - - +
132A ILE* 1.3 73.5 - - - +
134A TRP* 1.3 66.0 + - - +
135A VAL* 5.2 0.2 - - + -
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Residues in contact with TRP 134 (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 TYR* 3.4 28.3 - + + -
56A HIS 4.0 5.6 - - - -
57A TYR* 3.5 38.7 - + + -
105A PRO* 5.9 0.2 - - + -
108A ILE* 4.4 4.4 - - - +
109A GLY* 3.2 25.1 - - - +
110A ARG* 3.5 46.6 + - + +
132A ILE 4.2 1.6 + - - -
133A LYS* 1.3 82.4 - - - +
135A VAL* 1.3 75.0 + - - +
136A SER* 3.3 29.6 - - - -
137A CYS* 2.9 34.8 - - - -
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Residues in contact with VAL 135 (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 HIS* 3.2 29.0 + - + +
57A TYR 4.4 0.4 - - - -
58A GLU* 3.4 44.9 - - + +
110A ARG* 5.3 5.5 + - - -
133A LYS* 5.2 0.4 - - + -
134A TRP* 1.3 92.8 + - - +
136A SER* 1.3 74.1 + - - +
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Residues in contact with SER 136 (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 HIS* 3.0 48.4 + - - +
134A TRP* 3.3 20.3 - - - -
135A VAL* 1.3 88.2 - - - +
137A CYS* 1.3 66.4 + - - +
138A VAL* 4.5 3.8 - - - +
157A GLU* 5.5 2.9 + - - -
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Residues in contact with CYS 137 (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 ASP* 4.5 17.0 - - + +
54A ILE 3.7 6.1 - - - +
55A TYR* 4.0 18.2 - - - -
134A TRP* 2.9 32.4 - - - -
136A SER* 1.3 79.4 - - - +
138A VAL* 1.3 63.7 + - - +
139A SER 4.0 1.3 + - - -
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Residues in contact with VAL 138 (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 ASP* 3.5 1.9 - - - -
54A ILE* 2.7 62.8 + - + +
56A HIS* 4.2 24.0 - - + +
101A TYR* 4.6 10.3 - - + -
136A SER* 4.5 4.5 - - - +
137A CYS* 1.3 76.7 - - - +
139A SER* 1.3 60.6 + - - +
140A LEU* 3.5 1.3 + - + -
157A GLU* 4.7 14.4 - - + +
158A THR* 3.8 40.6 - - + +
161A ALA* 4.5 2.2 - - + -
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Residues in contact with SER 139 (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 ASP* 3.2 26.4 + - - +
137A CYS 4.0 2.6 + - - -
138A VAL* 1.3 70.9 - - - +
140A LEU* 1.3 62.4 + - - +
141A GLN* 3.0 10.3 - - - -
142A ALA* 3.1 35.3 + - - +
143A LEU 3.8 2.6 + - - -
158A THR* 4.1 11.0 + - - +
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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