Contacts of the strand formed by residues 169 - 178 (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 HIS 169 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23D LEU* 3.9 18.8 - - + +
28D ASN* 4.4 12.5 + - - -
29D VAL 3.0 25.7 + - - -
30D LYS* 3.8 8.7 + - - -
32D LYS* 3.4 35.4 + - + -
165D ASN* 2.9 21.4 + - - -
167D SER* 3.8 3.9 - - - -
168D GLY* 1.3 83.0 - - - +
170D ALA* 1.3 61.3 + - - +
171D ILE* 5.1 0.2 - - - +
58E ASP* 3.6 15.4 - - - +
79E ARG* 5.1 13.4 + - - -
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Residues in contact with ALA 170 (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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23D LEU* 3.7 3.5 - - - +
32D LYS 2.8 11.0 + - - +
33D ILE* 3.3 19.6 - - + -
34D ALA 2.9 26.5 + - - -
106D VAL* 3.8 22.2 - - + -
115D ASN* 4.3 7.2 - - - +
164D MET* 4.1 11.4 - - + -
165D ASN* 3.2 11.0 - - - +
167D SER 4.3 1.3 - - - +
169D HIS* 1.3 72.6 - - - +
171D ILE* 1.3 65.3 - - - +
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Residues in contact with ILE 171 (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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16D PHE* 4.7 4.9 - - + +
19D LEU* 3.7 31.9 - - + +
20D LYS* 4.1 35.9 - - + +
23D LEU* 4.1 15.0 - - + -
34D ALA* 3.7 4.0 - - + -
163D PHE* 3.5 2.1 - - + +
164D MET* 3.3 24.8 - - - +
165D ASN* 2.8 16.8 + - + +
169D HIS 5.1 0.9 - - - +
170D ALA* 1.3 78.4 - - - +
172D LEU* 1.3 63.9 + - - +
173D GLU 4.7 0.2 - - - +
58E ASP* 3.8 25.6 - - + +
60E VAL* 3.9 22.7 - - + -
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Residues in contact with LEU 172 (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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19D LEU* 3.9 3.1 - - - +
33D ILE* 4.2 12.6 - - + -
34D ALA 3.0 13.2 + - - +
35D VAL* 3.5 18.2 - - + -
36D GLY 3.0 25.8 + - - +
102D VAL* 4.4 6.3 - - + -
104D PHE* 4.3 19.1 - - + -
117D TRP* 3.8 39.3 - - + -
163D PHE 3.3 16.2 - - - +
164D MET* 4.0 7.9 - - + -
170D ALA 4.1 0.4 - - - -
171D ILE* 1.3 72.3 - - - +
173D GLU* 1.3 61.4 + - - +
174D ILE* 3.7 33.7 - - + -
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Residues in contact with GLU 173 (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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14D LEU* 4.1 17.8 - - + +
15D GLY* 4.2 10.1 - - - -
16D PHE 4.1 11.4 + - - -
19D LEU* 3.7 12.6 - - + +
36D GLY 3.7 3.1 - - - -
149D TRP* 3.9 19.2 - - + -
161D ARG* 3.8 0.5 + - - +
162D GLY* 3.0 3.3 - - - -
163D PHE* 2.8 39.2 + - + +
171D ILE 4.1 0.8 - - - -
172D LEU* 1.3 71.9 - - - +
174D ILE* 1.3 64.2 + - - +
175D HIS* 2.9 32.5 + - + +
60E VAL* 3.6 29.7 - - + +
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Residues in contact with ILE 174 (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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14D LEU* 4.2 1.0 - - - +
36D GLY 3.0 10.5 + - - +
37D ILE* 3.3 17.3 - - + -
38D ASP 2.9 24.1 + - - -
102D VAL* 3.6 34.3 - - + -
117D TRP* 4.1 11.4 - - + -
119D VAL* 3.8 24.7 - - + -
160D SER* 4.7 2.9 - - - -
161D ARG 3.2 10.3 - - - +
162D GLY* 4.3 0.9 - - - -
172D LEU* 3.7 28.3 - - + -
173D GLU* 1.3 79.2 - - - +
175D HIS* 1.3 75.7 + - - +
176D VAL* 4.2 13.7 - - + -
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Residues in contact with HIS 175 (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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11D GLY 5.0 1.8 - - - -
14D LEU* 4.4 15.2 - - + +
38D ASP* 3.1 36.9 + - + +
40D GLU* 5.7 0.4 - - - +
149D TRP* 4.5 1.6 - + - -
159D LYS 3.8 0.3 - - - +
160D SER* 3.7 1.7 - - - -
161D ARG* 2.6 81.7 + - - +
173D GLU* 2.9 35.6 + - + +
174D ILE* 1.3 78.5 - - - +
176D VAL* 1.3 63.0 + - - +
177D THR* 3.7 14.3 + - + +
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Residues in contact with VAL 176 (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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37D ILE* 4.6 2.5 - - + -
38D ASP 3.1 7.0 + - - +
40D GLU* 2.8 31.9 + - - +
41D SER* 3.3 14.5 + - - -
45D TRP* 3.6 38.1 - - + -
100D LEU* 4.0 19.3 - - + -
119D VAL* 4.7 1.6 - - + -
154D LEU* 4.3 12.8 - - + -
158D LEU* 4.2 17.3 - - + -
159D LYS 3.6 8.5 - - - +
160D SER* 4.6 3.6 - - - -
174D ILE* 4.2 15.2 - - + -
175D HIS* 1.3 73.9 - - - +
177D THR* 1.3 61.1 + - - +
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Residues in contact with THR 177 (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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40D GLU* 3.7 24.9 - - + -
41D SER* 4.4 4.5 - - - -
158D LEU* 3.5 3.8 - - - +
159D LYS* 2.9 50.5 + - - +
161D ARG* 5.8 4.1 - - + +
175D HIS* 4.1 19.0 + - + +
176D VAL* 1.3 79.7 - - - +
178D LYS* 1.3 71.6 + - - +
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Residues in contact with LYS 178 (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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40D GLU 3.4 24.4 + - - -
41D SER* 3.5 15.7 - - - +
42D GLY* 4.2 11.2 - - - -
67D HIS* 3.8 24.2 + - - -
157D GLY 3.7 7.2 - - - +
158D LEU* 4.6 3.1 - - + -
159D LYS* 3.8 5.2 + - - -
177D THR* 1.3 81.0 + - - +
179D ALA* 1.3 65.1 + - - +
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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