Contacts of the strand formed by residues 452 - 460 (chain D) in PDB entry 5MKF
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 452 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248C TYR* 3.3 42.4 - - + +
251C ARG* 3.9 13.2 - - - +
382D ILE* 4.5 13.5 - - + -
383D ILE* 5.6 3.4 - - + -
442D LEU 4.2 0.3 - - - +
443D VAL 3.6 1.0 - - - -
444D GLU* 2.8 62.4 + - + +
446D PRO* 4.0 18.6 - - + -
451D VAL* 1.3 86.0 - - - +
453D PRO* 1.3 74.0 - - + +
454D SER* 5.0 2.2 - - - -
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Residues in contact with PRO 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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251C ARG* 5.3 8.7 - - - +
270D PHE* 3.6 35.0 - - + +
271D LYS* 3.5 26.5 - - - +
273D LEU* 4.6 13.5 - - + +
442D LEU 4.3 1.8 - - - +
443D VAL* 4.7 6.5 - - + -
451D VAL* 3.8 15.9 - - + +
452D ILE* 1.3 97.4 - - + +
454D SER* 1.3 65.4 + - - +
455D TRP* 4.8 5.6 - - + -
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Residues in contact with SER 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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651A GLU* 6.1 1.4 - - - +
654A ARG* 4.0 19.3 + - - -
270D PHE* 3.5 11.4 - - - -
382D ILE* 5.8 3.8 - - - -
441D LEU* 4.1 0.5 - - - -
442D LEU* 2.9 54.5 + - - +
452D ILE* 5.0 3.4 - - - -
453D PRO* 1.3 78.1 - - - +
455D TRP* 1.3 87.1 + - - +
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Residues in contact with TRP 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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651A GLU* 2.4 50.7 + - + +
654A ARG* 5.9 0.2 + - - -
258D LEU* 4.3 25.5 - - + +
270D PHE* 3.8 18.4 - + + -
271D LYS* 3.6 47.6 - - + -
440D ARG 3.7 6.1 - - - -
441D LEU* 3.6 19.5 - - + +
442D LEU* 4.7 3.4 - - - +
453D PRO* 4.8 4.9 - - + -
454D SER* 1.3 99.3 + - - +
456D GLN* 1.3 69.2 + - - +
457D PHE* 4.8 15.3 - + + -
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Residues in contact with GLN 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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622A GLN* 3.1 23.2 + - - +
651A GLU 5.2 3.2 + - - -
652A ALA 4.5 12.8 + - - +
654A ARG* 5.3 6.1 - - - +
379D HIS* 5.5 9.8 + - - +
438D VAL 4.1 0.5 - - - +
439D VAL* 3.9 1.4 - - - -
440D ARG* 2.9 51.0 + - + +
442D LEU* 6.0 3.6 - - + -
455D TRP* 1.3 79.9 + - - +
457D PHE* 1.3 86.0 + - - +
458D GLN* 4.2 6.6 + - + +
556D ILE* 4.8 16.5 - - + +
1006D PX6 4.3 16.6 + - - -
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Residues in contact with PHE 457 (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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622A GLN* 2.7 34.8 + - + +
250D THR* 5.4 13.9 - - + +
253D MET* 4.2 12.6 - - + -
254D SER* 3.4 44.0 - - - -
257D PHE* 5.0 10.1 - + + -
258D LEU* 4.2 24.2 - - + -
437D CYS* 5.1 6.1 - - - -
438D VAL 3.9 1.6 - - - +
439D VAL* 3.7 39.3 - - + -
441D LEU* 4.3 11.9 - - + -
455D TRP* 4.8 12.0 - + + -
456D GLN* 1.3 86.8 + - - +
458D GLN* 1.3 57.5 + - - +
459D PRO* 3.8 4.9 - - - +
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Residues in contact with GLN 458 (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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621A THR* 5.2 3.6 + - - +
622A GLN* 4.4 7.3 + - - -
436D PHE 4.4 0.2 - - - +
437D CYS* 3.4 3.5 - - - -
438D VAL* 3.0 51.8 + - + +
456D GLN* 4.1 6.1 - - + +
457D PHE* 1.3 75.3 - - - +
459D PRO* 1.3 107.4 + - - +
460D LEU* 4.9 3.0 - - + +
552D ALA* 5.2 7.9 - - + +
555D GLN* 4.5 16.1 - - + +
556D ILE* 3.1 42.1 - - + +
559D ASN* 5.2 9.4 + - - +
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Residues in contact with PRO 459 (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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621A THR* 4.1 29.8 - - + +
622A GLN* 5.0 0.9 - - - +
242D MET* 5.9 1.7 - - - +
246D VAL* 4.4 15.3 - - + -
249D TYR* 5.0 2.9 - - + -
250D THR* 4.6 17.7 - - + -
435D LEU* 3.6 19.5 - - + -
437D CYS* 3.8 12.3 - - + -
457D PHE 3.8 8.5 - - - +
458D GLN* 1.3 126.7 + - - +
460D LEU* 1.3 64.8 + - - +
555D GLN* 4.6 0.5 - - - +
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Residues in contact with LEU 460 (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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242D MET* 5.5 4.7 - - + -
435D LEU* 3.3 9.3 - - - +
436D PHE* 2.5 53.2 + - - +
438D VAL* 6.1 0.9 - - + -
458D GLN* 4.9 4.3 - - + +
459D PRO* 1.3 78.3 - - - +
461D LYS* 1.3 84.6 + - + +
462D LEU* 4.0 7.2 - - + +
548D PHE* 3.4 33.4 - - + -
551D LEU 5.3 1.1 - - - +
552D ALA* 3.8 20.2 - - + -
555D GLN* 3.1 39.5 - - + +
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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