Contacts of the strand formed by residues 151 - 163 (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 SER 151 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145B TYR* 3.5 8.6 - - - -
146B HIS* 3.4 32.8 + - - -
149B ASN* 3.0 11.3 + - - -
150B LYS* 1.3 76.7 - - - +
152B TRP* 1.3 70.9 + - - +
153B MET* 4.1 6.9 - - - +
1305B NAG 3.1 28.8 + - - -
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Residues in contact with TRP 152 (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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143B VAL* 4.0 11.4 - - + -
144B TYR 3.7 4.5 - - - -
145B TYR* 3.5 56.7 - + + -
150B LYS* 5.3 0.8 - - - +
151B SER* 1.3 84.0 + - - +
153B MET* 1.3 61.0 + - - +
178B ASP 4.8 3.1 - - - +
179B LEU* 3.6 37.9 - - + +
180B GLU* 4.0 24.1 - - + +
181B GLY* 3.9 21.3 - - - -
245B HIS* 3.4 40.2 - + + -
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Residues in contact with MET 153 (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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143B VAL* 3.6 4.6 - - - +
144B TYR* 2.9 29.4 + - - +
146B HIS* 3.4 32.1 - - + +
151B SER* 4.1 6.5 - - - +
152B TRP* 1.3 74.5 - - - +
154B GLU* 1.3 63.7 + - - +
155B SER* 3.5 9.4 + - - +
179B LEU* 4.3 4.5 - - - -
1305B NAG 3.5 51.6 - - - +
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Residues in contact with GLU 154 (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* 3.3 21.8 + - - +
122B ASN* 4.1 11.5 - - - +
123B ALA* 2.9 43.2 + - + +
141B LEU* 3.9 16.1 - - - +
142B GLY 3.6 11.9 - - - +
143B VAL* 4.4 5.8 - - + +
153B MET* 1.3 76.7 - - - +
155B SER* 1.3 62.7 + - - +
156B GLU 3.9 16.3 - - - +
157B PHE* 4.4 4.7 - - - +
179B LEU* 4.1 8.0 - - + +
1N NAG 5.0 14.0 - - + +
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Residues in contact with SER 155 (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 2.8 12.4 + - - -
144B TYR* 3.4 29.1 - - - +
146B HIS* 5.8 0.3 - - - -
153B MET* 3.5 8.8 + - - +
154B GLU* 1.3 75.7 - - - +
156B GLU* 1.3 69.7 + - - +
157B PHE 4.2 0.3 + - - -
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Residues in contact with GLU 156 (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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140B PHE* 3.8 11.1 - - + -
141B LEU* 3.5 8.6 - - - +
142B GLY* 2.9 45.7 + - - +
154B GLU* 3.9 7.5 - - - +
155B SER* 1.3 86.0 - - - +
157B PHE* 1.3 61.6 + - - +
158B ARG* 3.3 44.5 + - + +
244B LEU* 5.2 1.4 - - - +
246B ARG* 3.1 44.7 + - - -
254B SER* 5.5 1.0 - - - -
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Residues in contact with PHE 157 (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 6.0 0.2 + - - -
118B LEU* 5.0 4.0 - - + -
120B VAL* 4.2 30.5 - - + -
122B ASN* 4.5 16.6 - - + -
141B LEU* 3.3 26.9 - - + -
154B GLU* 4.4 8.3 - - - +
155B SER 4.2 0.8 + - - -
156B GLU* 1.3 73.6 - - - +
158B ARG* 1.3 62.6 + - - +
159B VAL* 3.7 28.7 + - + -
160B TYR* 4.1 24.7 - + - +
1N NAG 5.7 3.8 - - - +
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Residues in contact with ARG 158 (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* 3.2 46.0 + - - +
15B CYS* 5.2 1.1 - - - -
16B VAL* 4.0 32.2 - - - +
136B CYS* 4.2 8.8 - - - -
138B ASP 4.3 1.1 - - - +
139B PRO* 3.2 6.4 - - - +
140B PHE* 2.9 52.4 + - + +
156B GLU* 3.3 36.1 + - + +
157B PHE* 1.3 79.8 + - - +
159B VAL* 1.3 59.9 + - - +
254B SER* 5.6 4.9 + - - -
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Residues in contact with VAL 159 (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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105B ILE* 4.7 1.8 - - + -
118B LEU* 4.3 7.6 - - + -
135B PHE* 3.4 29.2 - - + +
136B CYS* 2.8 26.9 + - - +
139B PRO* 4.0 15.0 - - + +
140B PHE 4.0 11.0 - - - +
141B LEU* 4.5 4.0 - - + -
157B PHE* 3.7 35.6 + - + -
158B ARG* 1.3 79.0 - - - +
160B TYR* 1.3 67.3 + - + +
241B LEU* 4.1 28.9 - - + -
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Residues in contact with TYR 160 (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 5.4 5.2 + - - -
15B CYS* 5.1 0.4 - - - -
118B LEU* 4.2 12.3 - - + -
129B LYS* 4.1 14.6 + - - +
133B PHE* 3.7 32.5 - + + -
134B GLN 3.5 13.9 - - - +
135B PHE* 3.9 13.5 - + + -
136B CYS* 4.1 7.1 - - - +
157B PHE* 4.1 23.1 - + - +
158B ARG* 5.8 0.3 - - - -
159B VAL* 1.3 93.0 + - + +
161B SER* 1.3 65.3 + - - +
162B SER* 3.9 16.4 - - - +
163B ALA* 4.5 12.6 - - + -
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Residues in contact with SER 161 (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* 6.0 3.7 - - - +
15B CYS* 3.8 19.6 - - - -
134B GLN* 2.9 29.8 + - - +
135B PHE 5.4 0.2 - - - -
160B TYR* 1.3 78.8 - - - +
162B SER* 1.3 61.6 + - - +
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Residues in contact with SER 162 (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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112B SER* 5.7 1.6 - - - -
132B GLU 3.6 2.2 + - - +
133B PHE* 3.4 4.9 - - - +
134B GLN* 3.1 37.2 + - - +
160B TYR* 3.7 6.9 - - - -
161B SER* 1.3 81.7 - - - +
163B ALA* 1.3 61.7 + - - +
164B ASN* 4.3 1.6 - - - -
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Residues in contact with ALA 163 (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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129B LYS* 4.9 5.4 - - - +
131B CYS* 4.1 12.3 - - + -
132B GLU 3.6 5.6 - - - -
133B PHE* 3.4 33.0 - - + -
160B TYR* 4.4 11.6 - - + -
162B SER* 1.3 74.7 - - - +
164B ASN* 1.3 63.7 + - - +
166B CYS* 4.6 4.1 - - - -
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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