Contacts of the strand formed by residues 133 - 146 (chain B) in PDB entry 6ZGI
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 133 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110B LEU* 4.1 2.6 - - - -
111B ASP 3.8 4.5 + - - -
112B SER* 3.0 22.4 + - - +
114B THR 4.7 1.7 + - - +
116B SER* 3.6 14.9 + - - -
118B LEU* 4.1 16.2 - - + -
129B LYS* 4.1 23.1 - - + -
131B CYS* 3.5 43.7 + - + -
132B GLU* 1.3 72.6 - - - +
134B GLN* 1.3 59.1 + - - +
135B PHE* 3.5 42.2 + + + +
160B TYR* 3.7 35.7 - + + -
162B SER 3.4 1.8 - - - -
163B ALA* 3.4 26.2 - - + -
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Residues in contact with GLN 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B LEU 4.9 0.8 + - - -
111B ASP* 3.0 25.0 - - - +
112B SER* 2.9 28.3 + - - +
132B GLU 4.0 0.4 + - - -
133B PHE* 1.3 69.0 - - - +
135B PHE* 1.3 72.1 + - - +
160B TYR* 4.1 1.6 - - - -
161B SER* 2.9 38.6 + - - +
162B SER* 3.1 26.3 + - - +
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Residues in contact with PHE 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B CYS* 5.1 0.2 - - - -
105B ILE* 3.7 42.6 - - + -
110B LEU* 4.0 43.5 + - + +
116B SER* 3.5 27.1 - - - -
117B LEU 4.9 0.4 - - - -
118B LEU* 4.7 6.5 - - + -
133B PHE* 3.5 42.5 + + + -
134B GLN* 1.3 86.6 + - - +
136B CYS* 1.3 69.6 + - - +
137B ASN 3.9 0.3 + - - -
139B PRO* 5.2 0.9 - - + -
159B VAL* 3.4 28.7 - - + +
160B TYR* 3.9 7.0 - + + -
161B SER* 5.4 0.2 - - - -
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Residues in contact with CYS 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B GLN 4.4 2.0 - - - -
15B CYS* 2.0 56.1 - - + -
135B PHE* 1.3 78.7 - - - +
137B ASN* 1.3 64.9 + - - +
138B ASP 3.4 17.6 + - - +
139B PRO* 3.5 14.6 - - + +
158B ARG* 4.2 11.7 - - - -
159B VAL 2.8 29.4 + - - +
160B TYR* 4.1 5.6 - - - -
239B GLN* 4.8 2.8 + - - -
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Residues in contact with ASN 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B CYS* 5.0 2.6 - - - +
17B ASN* 4.0 14.0 + - - +
135B PHE 3.9 1.0 + - - -
136B CYS* 1.3 73.6 - - - +
138B ASP* 1.3 58.4 + - - +
139B PRO* 3.7 5.0 - - - +
239B GLN* 4.5 9.0 + - - +
1M NAG 3.0 46.3 + - - +
2M NAG 5.2 6.0 - - - +
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Residues in contact with ASP 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B VAL 4.1 18.2 + - - +
17B ASN* 4.4 9.0 + - - +
18B LEU* 4.1 23.4 + - - +
21B ARG* 3.0 29.5 + - - -
79B PHE* 5.4 0.2 - - - -
81B ASN* 2.9 30.4 + - - +
136B CYS* 3.2 6.8 - - - +
137B ASN* 1.3 80.5 - - - +
139B PRO* 1.3 66.0 - - - +
140B PHE* 3.3 17.0 - - - -
158B ARG* 4.3 2.1 - - - +
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Residues in contact with PRO 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B ASN* 3.9 16.1 + - - +
105B ILE* 4.5 10.5 - - + -
135B PHE* 5.2 0.2 - - + -
136B CYS* 3.5 20.2 - - + +
137B ASN 3.7 1.3 - - - +
138B ASP* 1.3 87.3 - - - +
140B PHE* 1.3 65.7 + - - +
158B ARG 3.2 11.9 - - - +
159B VAL* 4.0 26.0 - - + +
239B GLN* 3.7 32.3 - - + +
240B THR 5.0 4.7 - - - +
241B LEU* 4.6 13.1 - - + -
242B LEU 5.0 5.2 + - - -
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Residues in contact with PHE 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B VAL* 3.5 38.1 - - + -
18B LEU* 4.2 27.6 - - + -
79B PHE* 4.7 6.7 - - + -
138B ASP* 3.3 24.2 - - - +
139B PRO* 1.3 76.0 - - - +
141B LEU* 1.3 85.7 + - - +
156B GLU* 3.8 25.1 - - + -
158B ARG* 2.9 52.3 + - + +
159B VAL* 4.0 2.0 - - - +
241B LEU* 5.6 0.7 - - - -
242B LEU 3.7 11.0 - - - +
244B LEU* 3.6 28.0 - - + -
246B ARG* 4.7 3.8 - - - -
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Residues in contact with LEU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ARG* 4.1 36.1 - - + +
120B VAL* 4.6 5.6 - - + -
121B ASN 5.5 0.4 - - - +
122B ASN* 5.7 0.9 - - + -
140B PHE* 1.3 95.6 - - - +
142B GLY* 1.3 59.5 + - - +
154B GLU* 3.9 8.7 - - - +
156B GLU 3.5 9.6 - - - +
157B PHE* 3.3 37.7 - - + -
159B VAL* 4.5 2.7 - - + -
241B LEU* 4.3 23.6 - - + -
242B LEU 3.1 19.6 + - - +
243B ALA* 3.3 11.7 - - + -
244B LEU* 2.9 23.6 + - - +
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Residues in contact with GLY 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B LEU* 1.3 76.8 - - - +
143B VAL* 1.3 58.3 - - - -
154B GLU* 3.6 6.8 - - - +
155B SER* 2.8 31.6 + - - -
156B GLU* 2.9 41.9 + - - +
244B LEU* 4.0 5.8 - - - -
246B ARG* 6.5 0.7 - - - -
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Residues in contact with VAL 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ARG* 3.7 26.2 - - - +
142B GLY* 1.3 75.1 - - - +
144B TYR* 1.3 64.1 + - - +
152B TRP* 4.0 35.6 - - + -
153B MET 3.6 12.3 - - - +
154B GLU* 4.7 6.1 - - + -
179B LEU* 4.6 14.4 - - + +
243B ALA* 4.6 8.5 - - + -
244B LEU 2.8 21.4 + - - +
245B HIS* 3.3 13.1 - - + +
246B ARG* 2.9 26.6 + - - +
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Residues in contact with TYR 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B GLY 4.2 0.6 + - - -
143B VAL* 1.3 77.0 - - - +
145B TYR* 1.3 69.4 + - - +
146B HIS* 3.3 42.1 + + + -
151B SER 4.0 1.2 - - - +
152B TRP* 3.7 3.3 - - - -
153B MET* 2.9 33.5 + - - +
155B SER* 3.4 25.1 - - - +
246B ARG* 3.4 34.1 - - + -
247B SER* 4.4 12.4 + - - -
248B TYR* 5.1 1.2 + - - +
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Residues in contact with TYR 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B TYR* 1.3 85.6 + - - +
146B HIS* 1.3 86.4 + - - +
147B LYS* 4.0 5.6 + - - +
150B LYS* 3.7 26.5 - - + +
151B SER 3.5 19.1 - - - -
152B TRP* 3.5 57.4 - + + -
246B ARG 2.8 15.4 + - - +
247B SER* 3.8 30.8 - - - -
248B TYR* 4.7 16.2 + + - -
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Residues in contact with HIS 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B TYR* 3.3 37.5 - + - -
145B TYR* 1.3 89.6 - - - +
147B LYS* 1.3 61.7 + - - +
148B ASN* 3.7 7.4 - - - +
149B ASN* 3.0 38.5 + - - +
150B LYS* 3.8 0.2 - - - -
151B SER* 3.4 15.6 + - - -
153B MET* 3.4 46.5 - - + +
1305B NAG 3.8 24.5 + - - -
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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