Contacts of the strand formed by residues 399 - 406 (chain D) in PDB entry 1I2M
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 ARG 399 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D LEU* 3.5 30.8 - - - +
38D LEU* 4.4 7.5 - - - +
62D LEU* 5.0 7.1 - - - +
364D GLY 4.6 1.9 - - - +
394D LYS 5.1 0.6 + - - -
395D GLN* 3.0 54.5 + - - +
396D LEU* 3.3 20.5 - - + +
397D GLU 3.1 7.2 + - - +
398D ASN* 1.3 86.1 - - + +
400D VAL* 1.3 70.3 + - - +
401D VAL* 5.7 0.3 - - - +
415D VAL* 3.9 17.9 - - + -
416D LYS 3.1 17.5 - - - +
417D ASP* 4.5 9.5 + - - +
418D LYS* 3.9 7.7 + - - +
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Residues in contact with VAL 400 (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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363D ASP 4.1 16.8 - - - +
364D GLY* 3.5 15.3 - - - +
396D LEU* 6.0 0.2 - - - -
399D ARG* 1.3 75.4 - - - +
401D VAL* 1.3 63.1 + - - +
402D LEU* 4.8 8.5 - - + -
415D VAL* 3.4 5.7 - - - +
416D LYS* 2.9 51.4 + - + +
417D ASP 4.1 9.6 - - - +
418D LYS* 3.5 35.4 - - + -
419D GLU 4.8 1.3 - - - +
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Residues in contact with VAL 401 (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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360D VAL* 3.4 34.2 - - + +
364D GLY* 2.8 27.8 + - - +
366D VAL* 3.9 30.5 - - + +
396D LEU* 4.1 20.9 - - + -
399D ARG 5.7 0.2 - - - +
400D VAL* 1.3 74.9 - - - +
402D LEU* 1.3 63.3 + - - +
403D SER 3.4 27.8 - - - +
413D LEU* 4.3 10.1 - - + -
414D LEU 3.8 5.4 - - - +
415D VAL* 4.2 4.9 - - + -
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Residues in contact with LEU 402 (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 GLU* 3.7 55.2 - - + +
34D PRO 4.0 6.7 - - - +
35D GLY* 4.3 0.2 - - - -
349D SER* 4.7 6.4 + - - -
360D VAL* 4.7 3.6 - - - +
400D VAL* 4.8 6.7 - - + -
401D VAL* 1.3 77.0 - - - +
403D SER* 1.3 65.0 + - - +
414D LEU* 2.8 33.6 + - + +
415D VAL 4.3 3.4 - - - -
416D LYS* 3.8 32.5 - - + +
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Residues in contact with SER 403 (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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71D GLN* 5.6 0.9 - - - +
72D ALA 4.8 11.3 + - - -
349D SER* 4.9 4.0 - - - -
360D VAL* 4.4 6.3 - - - -
401D VAL* 3.4 14.1 - - - +
402D LEU* 1.3 82.8 - - - +
404D VAL* 1.3 63.8 + - - +
413D LEU* 3.5 1.6 - - - -
414D LEU* 3.0 45.9 + - - +
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Residues in contact with VAL 404 (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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72D ALA 5.3 0.2 - - - -
73D GLU* 5.6 0.2 - - - +
349D SER* 5.3 1.1 + - - +
350D VAL 5.2 2.0 - - - -
351D ALA* 3.4 20.6 - - + +
358D TYR* 3.8 40.6 - - + -
360D VAL* 3.6 24.0 - - + +
366D VAL* 4.5 2.7 - - + -
403D SER* 1.3 80.3 - - - +
405D SER* 1.3 65.6 + - - +
411D THR* 3.7 19.5 - - + -
412D VAL 3.4 4.5 - - - -
413D LEU* 3.5 24.0 - - + -
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Residues in contact with SER 405 (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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72D ALA 3.5 23.6 - - - -
73D GLU* 3.4 17.7 + - - -
74D ALA* 2.8 31.3 + - - +
351D ALA* 4.6 5.2 - - - -
404D VAL* 1.3 76.9 - - - +
406D SER* 1.3 62.5 + - - +
411D THR* 3.5 2.8 - - - +
412D VAL* 2.8 34.1 + - - +
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Residues in contact with SER 406 (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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74D ALA* 3.6 11.6 - - - +
351D ALA* 5.1 1.4 - - - +
352D CYS 3.5 16.4 + - - +
353D GLY* 3.3 21.7 - - - -
358D TYR* 3.5 24.7 - - - -
376D GLN* 3.2 13.7 + - - -
405D SER* 1.3 78.5 + - - +
407D GLY* 1.3 63.8 + - - +
410D HIS 3.7 3.4 - - - -
411D THR* 3.0 17.9 + - - -
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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