Contacts of the strand formed by residues 162 - 168 (chain D) in PDB entry 1CD9
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 162 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A SER* 6.5 0.4 - - - -
125A LEU 4.8 6.7 + - - +
151D ARG* 3.4 3.3 - - - -
152D TYR* 2.9 82.4 + - + +
153D GLN* 5.5 0.2 - - - -
160D ASN 3.7 5.0 + - - -
161D TRP* 1.3 74.0 + - - +
163D LEU* 1.3 67.2 + - - +
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Residues in contact with LEU 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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9A SER* 3.7 24.1 - - - +
70A LEU* 5.6 0.3 - - - +
124A GLU 5.8 1.3 - - - +
125A LEU* 4.6 17.3 + - + +
149D GLU* 4.0 19.7 - - + +
150D LEU 3.7 4.7 - - - +
151D ARG* 4.1 10.1 - - + -
161D TRP* 4.1 20.2 - - + +
162D THR* 1.3 85.0 - - - +
164D VAL* 1.3 65.8 + - - +
165D PHE* 3.7 37.9 - - + -
203D TRP* 4.2 18.6 - - + -
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Residues in contact with VAL 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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7A ALA* 3.5 32.3 - - + -
8A SER 3.7 6.7 - - - +
70A LEU* 4.6 19.5 - - + -
148D CYS 4.3 0.3 - - - +
149D GLU* 3.4 6.8 - - - +
150D LEU* 3.1 38.0 + - + +
152D TYR* 3.8 26.9 - - + -
163D LEU* 1.3 77.5 - - - +
165D PHE* 1.3 61.6 + - - +
167D LEU* 3.9 20.0 - - + +
174D PHE* 4.7 6.7 - - + -
176D LEU* 4.8 4.9 - - + -
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Residues in contact with PHE 165 (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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7A ALA* 3.3 5.2 - - - +
8A SER 2.8 39.8 + - - +
9A SER* 3.3 19.1 - - - -
10A LEU 3.6 11.2 - - - +
11A PRO* 3.6 27.1 - - + -
125A LEU* 3.6 23.6 - - + -
148D CYS 3.9 1.6 - - - -
149D GLU* 3.8 28.0 - - + -
163D LEU* 3.7 29.8 - - + -
164D VAL* 1.3 75.8 - - - +
166D HIS* 1.3 89.5 + - + +
167D LEU 3.2 3.2 + - - -
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Residues in contact with HIS 166 (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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6A PRO* 3.3 37.8 - - + +
8A SER* 5.5 3.8 - - - -
10A LEU 4.3 5.4 - - - -
11A PRO* 4.0 2.0 - - - +
12A GLN* 3.1 51.2 + - + +
175A PRO* 6.2 0.2 - - + -
147D GLU* 3.3 43.6 + - + +
148D CYS 3.4 6.9 + - - -
149D GLU* 5.1 1.8 - - - +
165D PHE* 1.3 88.8 - - + +
167D LEU* 1.3 63.4 + - - +
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Residues in contact with LEU 167 (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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5A GLY* 5.3 2.7 - - - -
7A ALA* 3.5 25.8 - - + +
135D TRP* 3.9 22.9 - - + -
147D GLU* 3.5 5.5 - - - +
148D CYS* 2.7 40.3 + - + +
149D GLU 4.7 0.2 - - - -
150D LEU* 3.5 38.8 - - + +
164D VAL* 3.9 20.4 - - + +
165D PHE 3.2 1.2 + - - +
166D HIS* 1.3 76.8 - - - +
168D PRO* 1.3 79.1 - - + +
174D PHE* 4.0 17.9 - - + -
189D MET* 4.3 4.0 - - + -
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Residues in contact with PRO 168 (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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5A GLY* 4.1 15.9 - - - -
6A PRO* 4.2 7.8 - - + -
135D TRP* 2.8 23.9 + - + -
146D GLN 4.7 2.7 - - - +
148D CYS* 3.9 5.3 - - - -
166D HIS 4.2 2.9 - - - +
167D LEU* 1.3 103.5 - - + +
169D SER* 1.3 60.7 + - - +
170D SER 3.1 9.0 - - - +
171D LYS* 3.7 36.3 - - + -
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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