Contacts of the strand formed by residues 452 - 456 (chain D) in PDB entry 5IWM
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 GLN 452 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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421D CYS* 3.8 7.0 - - - +
430D GLU* 3.5 23.3 + - + -
432D PHE* 3.9 24.0 - - + -
447D ARG* 2.9 46.5 + - + +
448D ASP* 2.8 43.3 + - - +
449D SER* 4.2 0.3 - - - -
451D THR* 1.3 84.7 - - - +
453D ALA* 1.3 59.0 + - - +
454D ILE* 5.6 0.2 - - + -
592D TRP* 3.9 8.3 - - - -
596D MET* 3.1 32.6 + - + +
598D PRO* 4.4 5.9 - - - +
601D ARG* 3.7 2.4 - - - +
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Residues in contact with ALA 453 (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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418D LEU* 4.4 2.2 - - + -
419D ALA 3.7 8.3 - - - +
420D ASP* 3.8 10.1 - - - +
421D CYS* 4.1 4.2 - - - +
430D GLU 2.7 16.8 + - - +
431D ILE* 3.9 8.5 - - + -
432D PHE* 2.8 31.6 + - - -
447D ARG* 4.2 0.2 - - - +
451D THR 3.9 1.0 + - - -
452D GLN* 1.3 73.9 - - - +
454D ILE* 1.3 61.5 + - - +
500D TYR* 3.5 35.2 - - + +
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Residues in contact with ILE 454 (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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418D LEU* 3.8 2.8 - - - +
419D ALA* 2.9 37.1 + - + +
431D ILE* 4.7 0.2 - - - -
432D PHE* 3.5 11.9 - - + +
434D VAL* 4.4 10.8 - - + -
440D GLY* 4.8 1.1 - - - +
443D THR* 3.4 41.5 - - + +
444D LYS* 3.5 43.7 - - + -
447D ARG* 3.6 22.0 - - + +
452D GLN 4.3 2.2 - - - +
453D ALA* 1.3 82.2 - - - +
455D LEU* 1.3 63.6 + - - +
456D PRO* 3.7 14.0 - - + +
596D MET* 5.1 2.0 - - + -
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Residues in contact with LEU 455 (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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417D LYS 4.3 1.1 - - - -
418D LEU* 4.2 25.4 - - + +
431D ILE* 4.1 10.5 - - + +
432D PHE 3.0 8.8 + - - -
433D LEU* 3.7 21.4 - - + +
434D VAL 3.5 17.9 + - - +
454D ILE* 1.3 75.0 - - - +
456D PRO* 1.3 69.5 - - - +
457D LEU* 3.7 11.5 + - + +
480D GLN* 3.6 45.1 - - + +
481D MET* 3.9 31.0 - - + -
484D ALA* 4.0 10.8 - - + -
485D PHE* 5.9 0.2 - - + -
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Residues in contact with PRO 456 (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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417D LYS* 3.6 26.1 - - + +
434D VAL* 3.6 13.9 - - + -
436D GLY 3.6 25.8 - - - +
437D ASP* 3.6 20.4 - - - +
440D GLY* 4.8 1.6 - - - -
444D LYS* 4.2 17.7 - - - +
454D ILE* 3.7 11.2 - - + +
455D LEU* 1.3 96.7 - - - +
457D LEU* 1.3 62.3 + - - +
458D ARG* 4.0 8.1 + - - +
480D GLN* 4.5 4.5 - - - +
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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