Contacts of the strand formed by residues 3 - 11 (chain D) in PDB entry 1XPM
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 ILE 3 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320B GLU* 3.7 24.7 + - + +
2D ALA* 1.3 81.1 - - - +
4D GLY* 1.3 61.6 + - - +
122D LYS* 3.7 51.1 - - + +
125D LEU* 4.2 7.4 - - + -
126D ALA* 4.0 13.5 - - + +
162D ILE* 4.1 7.6 - - + -
163D ALA 3.4 15.3 - - - +
164D HIS* 3.7 31.0 - - + +
166D PRO* 3.9 4.3 - - - -
170D ALA* 3.8 0.2 - - - -
171D LEU* 2.9 30.9 + - - +
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Residues in contact with GLY 4 (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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3D ILE* 1.3 78.9 - - - +
5D ILE* 1.3 65.4 + - - -
6D ASP 3.3 0.3 + - - -
162D ILE* 3.2 10.4 - - - -
163D ALA 2.9 33.4 + - - +
166D PRO* 3.5 5.2 - - - +
169D LEU 3.2 11.9 - - - -
171D LEU* 3.9 16.2 - - - -
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Residues in contact with ILE 5 (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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4D GLY* 1.3 68.3 - - - -
6D ASP* 1.3 57.9 + - - +
7D LYS 3.5 23.6 - - - +
8D ILE* 4.0 19.3 - - + -
118D ILE* 4.6 11.2 - - + -
160D MET* 4.0 19.3 - - + -
161D VAL 3.7 4.5 - - - +
162D ILE* 3.9 17.7 - - + -
166D PRO* 3.4 3.0 - - - +
168D ILE* 3.3 16.6 + - + +
169D LEU* 2.9 45.6 + - + +
171D LEU* 4.7 12.1 - - + +
282D TYR* 5.2 0.4 - - + -
285D LEU* 3.8 28.3 - - + -
289D LEU* 6.3 0.4 - - + -
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Residues in contact with ASP 6 (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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4D GLY 3.3 1.2 + - - -
5D ILE* 1.3 74.1 - - - +
7D LYS* 1.3 83.9 + - + +
132D LYS* 3.8 19.3 + - - -
161D VAL* 2.8 18.4 + - + +
163D ALA* 4.2 21.1 - - + -
164D HIS 5.4 0.7 - - - -
165D ASN 4.0 3.5 - - - +
166D PRO* 3.6 7.0 - - + +
167D SER* 2.8 45.0 + - - +
168D ILE* 3.6 15.1 - - - +
325D HIS* 4.7 0.2 - - - +
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Residues in contact with LYS 7 (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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5D ILE* 3.5 6.3 - - - +
6D ASP* 1.3 99.9 - - + +
8D ILE* 1.3 64.9 + - - +
62D ILE* 4.0 43.3 - - + +
67D ASP* 5.8 1.8 - - - +
160D MET* 3.4 2.3 - - - -
161D VAL* 3.0 36.7 + - + -
167D SER* 5.6 0.7 - - - +
168D ILE* 4.0 4.3 - - - -
325D HIS* 3.2 37.5 + - + +
327D ASP* 4.0 12.7 + - - -
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Residues in contact with ILE 8 (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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5D ILE* 4.0 9.4 - - + -
7D LYS* 1.3 80.1 - - - +
9D ASN* 1.3 68.0 + - - +
62D ILE* 4.1 6.4 - - - +
158D VAL* 4.1 3.6 - - + -
159D ALA 3.2 12.6 - - - +
160D MET* 3.7 24.7 - - + -
168D ILE* 4.0 18.7 - - + +
282D TYR* 4.0 10.3 - - + +
285D LEU* 4.3 18.4 - - + -
286D ILE* 3.5 34.8 - - + +
289D LEU* 4.7 8.3 - - + -
325D HIS 5.5 1.8 + - - +
326D LEU* 4.7 12.3 - - + -
327D ASP* 4.6 6.9 + - - +
331D HIS* 4.4 8.7 - - + -
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Residues in contact with ASN 9 (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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8D ILE* 1.3 77.3 - - - +
10D PHE* 1.3 77.3 + - - +
57D ASN 4.2 1.0 + - - -
58D ALA* 2.8 30.1 + - - +
61D ASP* 4.1 25.0 + - - +
62D ILE* 3.8 17.9 - - + -
158D VAL* 3.3 6.2 - - - +
159D ALA 2.8 30.4 + - - +
286D ILE* 3.8 7.9 - - - -
327D ASP* 5.3 4.0 - - - +
330D ALA* 5.8 0.7 - - - +
331D HIS* 2.6 33.7 + - - -
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Residues in contact with PHE 10 (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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9D ASN* 1.3 93.6 + - - +
11D TYR* 1.3 65.2 + - - +
12D VAL* 3.9 23.1 - - + -
58D ALA* 4.1 4.7 - - - -
157D ALA 3.1 14.1 - - - +
158D VAL* 3.9 15.0 - - + -
269D TYR* 4.1 13.7 - + + -
273D VAL* 5.0 1.1 - - + -
276D ILE* 6.0 0.9 - - + -
283D LEU* 3.8 26.2 - - + -
286D ILE* 3.8 17.0 - - + -
331D HIS* 3.6 36.3 - + + -
334D LEU* 3.5 31.6 - - + +
335D LEU* 4.2 25.1 - - + -
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Residues in contact with TYR 11 (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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10D PHE* 1.3 76.3 - - - +
12D VAL* 1.3 88.7 + - - +
13D PRO* 4.1 8.9 - - + +
14D LYS* 4.5 6.8 + - - +
49D GLN* 3.6 26.7 + - - +
54D MET* 3.8 23.3 - - + +
57D ASN* 3.6 32.1 - - + -
58D ALA* 3.8 20.6 - - + +
156D GLY* 3.2 4.0 - - - -
157D ALA 2.8 30.6 + - - +
334D LEU* 4.0 19.3 - - + -
371D ILE* 3.5 28.2 - - + +
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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