Contacts of the strand formed by residues 120 - 127 (chain Z) in PDB entry 5GGR
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 THR 120 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69Z ARG* 3.4 5.4 - - - +
70Z MET* 3.1 43.5 + - + +
119Z GLY* 1.3 73.2 - - - -
121Z TYR* 1.3 65.8 + - - +
139Z ARG* 3.4 43.7 - - + -
140Z ALA 3.3 11.4 - - - +
141Z GLU* 4.3 10.1 - - + +
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Residues in contact with TYR 121 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37Z PHE* 4.4 11.2 - - + -
52Z PHE* 5.0 5.6 - + + -
67Z TRP* 3.5 28.7 - + + +
68Z TYR 3.3 19.5 - - - -
69Z ARG* 3.3 21.4 + - + +
79Z LEU* 3.6 18.4 - - + -
95Z PHE* 4.8 10.9 - + - -
110Z VAL* 5.0 3.2 - - + +
117Z ASP* 2.3 43.5 + - - +
119Z GLY* 3.1 31.9 - - - -
120Z THR* 1.3 74.5 - - - +
122Z LEU* 1.3 65.2 + - - +
139Z ARG* 3.7 1.9 - - - -
140Z ALA* 2.4 46.3 + - - +
141Z GLU 5.1 0.2 - - - -
142Z LEU* 4.1 25.9 - - + +
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Residues in contact with LEU 122 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37Z PHE* 3.9 8.4 - - - -
67Z TRP* 3.0 9.1 - - - -
68Z TYR* 2.8 64.8 + - + +
70Z MET* 3.6 21.5 - - + -
76Z THR* 4.6 4.7 - - + -
121Z TYR* 1.3 78.0 - - - +
123Z CYS* 1.3 70.8 + - - +
136Z GLU* 4.4 15.9 - - + +
137Z SER* 3.5 10.3 - - - +
138Z LEU 4.5 6.7 - - - +
139Z ARG* 3.3 46.9 - - - +
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Residues in contact with CYS 123 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35Z PRO* 4.1 7.4 - - - -
37Z PHE* 3.5 13.9 - - + -
54Z CYS* 2.1 46.7 - - - -
65Z LEU* 5.5 2.2 - - - -
66Z ASN 3.1 17.7 - - - +
108Z MET* 3.6 11.9 - - + -
122Z LEU* 1.3 82.3 - - - +
124Z GLY* 1.3 53.9 + - - +
136Z GLU* 3.6 0.7 - - - -
137Z SER* 2.5 59.3 + - - -
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Residues in contact with GLY 124 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35Z PRO* 4.1 3.1 - - - -
64Z VAL 3.7 1.0 - - - +
65Z LEU* 4.6 3.4 - - - -
66Z ASN* 3.0 37.9 + - - +
68Z TYR* 5.3 4.7 - - - -
122Z LEU* 4.8 1.4 - - - +
123Z CYS* 1.3 77.0 - - - +
125Z ALA* 1.3 61.6 + - - -
126Z ILE* 4.3 4.2 - - - +
134Z ILE* 5.0 4.9 - - - -
135Z LYS 3.0 14.1 - - - -
136Z GLU* 4.0 6.7 - - - -
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Residues in contact with ALA 125 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32Z TRP* 3.5 11.1 - - + -
35Z PRO* 4.2 1.9 - - + +
56Z PHE* 3.5 41.3 - - + -
63Z PHE* 4.6 2.5 - - + -
64Z VAL 3.5 5.4 - - - +
65Z LEU* 3.6 15.3 - - + -
124Z GLY* 1.3 73.2 - - - -
126Z ILE* 1.3 61.4 + - - +
134Z ILE* 3.3 6.2 - - - +
135Z LYS 3.0 31.7 + - - +
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Residues in contact with ILE 126 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32Z TRP* 4.4 0.4 - - - -
63Z PHE* 3.2 7.2 - - - +
64Z VAL* 2.9 47.1 + - + +
66Z ASN* 4.1 13.9 - - - +
68Z TYR* 3.7 22.0 - - - +
124Z GLY 4.3 4.9 - - - +
125Z ALA* 1.3 82.3 - - - +
127Z SER* 1.3 76.1 + - - +
132Z ALA* 3.6 11.7 - - + -
133Z GLN 3.5 11.7 - - - +
134Z ILE* 3.7 22.0 - - + -
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Residues in contact with SER 127 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100H ASP* 5.0 2.0 + - - -
56L THR* 4.7 1.6 + - - -
32Z TRP* 4.3 3.1 - - - -
61Z GLU* 4.5 7.6 - - - -
63Z PHE* 3.4 27.9 - - - -
126Z ILE* 1.3 82.8 - - - +
128Z LEU* 1.3 62.4 + - - +
129Z ALA* 3.3 12.5 + - - +
131Z LYS 4.6 0.2 + - - -
132Z ALA* 3.2 25.1 - - - +
133Z GLN* 2.8 42.8 + - - +
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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