Contacts of the helix formed by residues 14 - 22 (chain J) in PDB entry 4XLN
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 14 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12J LEU 3.9 0.4 + - - -
13J ALA* 1.3 75.7 - - - +
15J PRO* 1.3 70.5 - - - +
16J GLU* 3.3 19.3 + - - +
17J LYS* 3.0 31.6 + - - +
18J ILE* 3.2 11.5 + - - +
511J TRP* 3.4 43.1 - - - -
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Residues in contact with PRO 15 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13J ALA 3.8 1.1 - - - +
14J SER* 1.3 84.5 - - - +
16J GLU* 1.3 67.4 + - - +
18J ILE* 3.3 14.2 + - + +
19J ARG* 2.9 52.1 + - - +
511J TRP* 4.2 17.7 - - + -
513J ILE 5.1 4.7 - - - +
514J LEU* 3.8 21.3 - - + -
515J GLU* 4.0 21.1 - - + +
516J ALA* 4.1 6.9 - - + +
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Residues in contact with GLU 16 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14J SER* 3.3 21.9 - - - +
15J PRO* 1.3 85.5 - - + +
17J LYS* 1.3 57.1 + - - +
19J ARG* 3.3 19.6 - - - +
20J SER* 2.9 30.8 + - - +
511J TRP* 4.9 4.4 + - - -
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Residues in contact with LYS 17 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1098I ASP* 4.3 20.6 - - - +
13J ALA* 4.6 2.0 - - + -
14J SER* 3.0 27.9 + - - +
16J GLU* 1.3 76.0 - - - +
18J ILE* 1.3 59.9 + - - +
20J SER* 3.0 11.8 + - - +
21J TRP* 2.9 68.8 + - + +
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Residues in contact with ILE 18 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1096I ALA* 3.8 9.0 - - + -
13J ALA* 4.1 4.9 - - + +
14J SER 3.2 12.7 + - - +
15J PRO* 3.6 5.8 - - + +
17J LYS* 1.3 71.6 - - - +
19J ARG* 1.3 60.9 + - - +
21J TRP* 3.3 23.6 + - + +
22J SER* 3.0 27.8 + - - -
91J GLY 4.6 1.5 - - - +
92J HIS* 3.9 12.6 - - + -
514J LEU* 3.6 24.2 - - + -
516J ALA* 3.2 32.1 - - + +
518J PRO* 3.6 44.6 - - + -
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Residues in contact with ARG 19 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1118I LYS* 3.7 5.9 + - - -
15J PRO* 2.9 46.8 + - - +
16J GLU* 3.3 22.5 - - - +
17J LYS 3.2 0.2 - - - -
18J ILE* 1.3 76.3 - - - +
20J SER* 1.3 61.2 + - - +
22J SER* 3.3 19.1 + - - +
92J HIS* 4.1 13.6 + - + +
94J GLU* 3.0 45.3 + - - +
515J GLU* 3.9 14.1 + - - +
516J ALA* 4.2 2.6 - - + +
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Residues in contact with SER 20 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1118I LYS* 3.3 30.9 - - - +
16J GLU* 2.9 16.0 + - - +
17J LYS* 3.0 19.8 + - - +
19J ARG* 1.3 73.7 - - - +
21J TRP* 1.3 68.9 + - - +
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Residues in contact with TRP 21 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090I LYS* 5.9 2.0 - - - -
1093I GLN* 3.1 55.2 + - - -
1096I ALA* 4.6 0.2 - - - -
1097I LEU 4.0 4.5 - - - -
1098I ASP* 3.4 20.3 + - - -
1116I ALA 5.2 2.7 - - - +
1118I LYS* 5.5 0.2 - - - +
13J ALA* 3.5 22.9 - - + -
17J LYS* 2.9 46.8 + - + +
18J ILE* 3.7 28.3 - - + +
19J ARG 3.3 0.2 - - - -
20J SER* 1.3 82.4 - - - +
22J SER* 1.3 63.5 + - - +
23J TYR* 3.4 17.3 - - - -
90J MET* 3.2 41.6 + - + +
91J GLY 5.8 0.9 - - - +
518J PRO* 4.8 2.7 - - + -
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Residues in contact with SER 22 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1118I LYS* 3.0 26.0 + - - -
18J ILE 3.0 18.2 + - - -
19J ARG 3.4 6.4 - - - +
20J SER 3.3 0.6 - - - -
21J TRP* 1.3 77.1 - - - +
23J TYR* 1.3 60.3 + - - +
24J GLY 2.8 17.0 + - - -
90J MET 3.2 8.1 - - - -
91J GLY* 3.3 2.6 - - - -
92J HIS* 2.5 49.3 + - - -
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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