Contacts of the strand formed by residues 158 - 164 (chain D) in PDB entry 3ZWG
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 LEU 158 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41D SER* 3.5 44.4 - - - +
43D LYS* 4.6 9.6 - - + -
94D MET* 3.8 36.8 - - + -
96D ASP* 5.7 0.2 - - - +
121D VAL* 4.4 11.0 - - + -
153D GLY* 3.9 1.2 - - - -
154D LEU* 2.9 30.7 + - + -
155D GLY 2.8 13.2 + - - +
156D TYR* 3.7 13.5 - - + +
157D GLY* 1.3 87.3 - - - +
159D LYS* 1.3 62.6 + - - +
176D VAL* 4.2 9.9 - - + -
177D THR 3.5 7.2 - - - +
178D LYS* 4.6 2.5 - - + -
179D ALA* 3.7 6.4 - - - +
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Residues in contact with LYS 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D SER* 5.3 11.2 - - - -
152D ARG 3.7 13.5 - - - +
153D GLY* 3.9 8.3 - - - -
154D LEU* 3.9 6.3 - - - +
158D LEU* 1.3 74.4 - - - +
160D SER* 1.3 65.1 + - - +
161D ARG* 6.1 5.4 - - + +
175D HIS 3.8 0.7 - - - +
176D VAL* 3.6 2.6 - - - +
177D THR* 2.9 50.7 + - - +
178D LYS 3.8 9.5 + - - -
179D ALA* 3.7 27.8 + - + +
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Residues in contact with SER 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D TRP* 4.9 4.3 - - - -
119D VAL* 3.6 42.4 + - - +
143D PHE* 5.1 3.5 - - - -
150D HIS 3.6 1.4 - - - +
151D SER* 3.1 7.2 - - - -
152D ARG* 2.9 44.4 + - - +
154D LEU* 3.8 11.5 - - - +
159D LYS* 1.3 76.6 - - - +
161D ARG* 1.3 61.8 + - - +
174D ILE* 4.7 2.0 - - - -
175D HIS 3.7 5.2 - - - -
176D VAL* 4.6 5.2 - - - +
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Residues in contact with ARG 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D TRP* 4.5 1.3 - - - -
149D TRP* 3.4 27.7 - - + -
150D HIS 3.6 4.3 - - - +
151D SER* 3.7 18.2 - - - +
159D LYS* 6.1 5.4 - - + +
160D SER* 1.3 74.5 - - - +
162D GLY* 1.3 58.8 + - - +
173D GLU* 3.8 0.5 + - - +
174D ILE* 3.2 2.9 - - - +
175D HIS* 2.6 87.9 + - + +
177D THR* 5.8 4.6 - - + +
63E HIS* 2.7 65.6 + - + +
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Residues in contact with GLY 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D TRP* 3.4 25.1 - - - -
148D GLY 3.9 0.3 - - - +
149D TRP* 3.3 8.2 - - - -
150D HIS 2.9 34.1 + - - -
161D ARG* 1.3 77.9 - - - +
163D PHE* 1.3 59.8 + - - -
173D GLU 3.0 11.0 - - - -
174D ILE* 4.0 4.5 - - - -
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Residues in contact with PHE 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D TRP* 4.2 2.1 - - - -
147D ASN* 3.3 47.1 - - + -
148D GLY* 3.4 18.6 - - - -
149D TRP* 3.5 40.2 - + + -
162D GLY* 1.3 73.7 - - - -
164D MET* 1.3 72.5 + - - +
165D ASN* 4.3 2.9 - - + -
171D ILE 3.5 2.2 - - - +
172D LEU* 3.3 9.2 - - - +
173D GLU* 2.8 31.3 + - + +
59E ILE 3.5 26.2 - - - -
60E VAL* 3.6 24.0 - - + -
61E LEU* 3.8 18.6 - - + -
73E TYR* 5.0 1.6 - - - -
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Residues in contact with MET 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D ILE* 3.9 28.3 - - + -
104D PHE* 4.8 1.6 - - + -
105D SER 4.1 5.8 - - - +
106D VAL* 3.9 18.2 - - + -
115D ASN* 4.1 9.6 - - - -
116D TRP 3.7 32.3 - - - +
117D TRP* 3.4 34.9 - - + +
145D GLY* 3.3 11.1 - - - -
146D ASP* 3.5 0.5 + - - +
147D ASN* 3.1 23.9 + - - -
148D GLY 4.3 3.1 + - - -
163D PHE* 1.3 81.9 - - - +
165D ASN* 1.3 69.2 + - - +
170D ALA* 4.1 7.0 - - + -
171D ILE 3.3 12.8 - - - +
172D LEU* 4.0 6.7 - - + -
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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