Contacts of the strand formed by residues 415 - 420 (chain D) in PDB entry 1F6A
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 THR 415 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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375D SER 4.2 0.2 - - - +
376D ARG* 3.6 2.4 - - - -
377D ALA* 2.9 61.3 + - + +
413D GLY 4.4 3.4 - - - +
414D GLU* 1.3 89.7 + - - +
416D TYR* 1.3 66.8 + - - +
417D GLN* 5.7 0.7 - - - +
432D SER* 4.8 6.9 - - - -
433D THR 3.9 0.2 - - - -
434D THR* 2.9 26.7 - - - +
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Residues in contact with TYR 416 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340D LEU* 4.3 1.7 - - - +
356D ILE* 3.7 25.8 - - + -
374D TRP* 5.1 3.6 - - + -
375D SER 3.6 5.4 - - - +
376D ARG* 3.3 36.9 + - + -
382D VAL* 5.1 4.0 - - + -
403D LEU* 4.8 9.0 - - + -
405D VAL* 3.2 38.5 - - + +
406D GLY 4.2 3.5 + - - -
409D ASP* 3.7 23.9 - - - +
410D TRP* 3.8 31.7 + + - -
414D GLU* 3.7 17.9 - - + +
415D THR* 1.3 75.3 - - - +
417D GLN* 1.3 61.0 + - - +
432D SER* 3.2 4.8 - - - -
433D THR* 3.0 32.9 + - + +
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Residues in contact with GLN 417 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340D LEU* 5.0 0.7 - - - -
373D THR 3.7 0.3 - - - +
374D TRP* 3.7 11.1 - - - -
375D SER* 2.9 48.0 + - - +
376D ARG 6.3 0.2 - - - -
415D THR* 5.7 1.1 - - - +
416D TYR* 1.3 76.8 - - - +
418D CYS* 1.3 69.1 + - - +
419D ARG* 4.1 5.1 + - - +
430D MET* 3.8 31.0 - - - +
431D ARG 3.3 15.2 - - - +
432D SER* 3.9 13.7 - - - -
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Residues in contact with CYS 418 (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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340D LEU* 4.2 6.7 - - + +
358D CYS* 2.0 53.8 - - + -
372D LEU* 3.3 24.2 - - - -
373D THR 3.9 2.5 - - - -
374D TRP* 4.1 13.5 - - + -
417D GLN* 1.3 72.1 - - - +
419D ARG* 1.3 58.7 + - - +
420D VAL* 4.1 7.1 + - - +
429D LEU 3.8 0.9 - - - +
430D MET* 3.3 6.6 - - - +
431D ARG* 2.8 33.6 + - + +
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Residues in contact with ARG 419 (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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371D ASN* 3.6 3.8 - - - +
372D LEU* 4.4 0.4 - - - -
373D THR* 3.0 50.6 + - + +
375D SER* 5.7 2.5 - - - +
417D GLN* 5.1 5.6 - - - +
418D CYS* 1.3 73.3 - - - +
420D VAL* 1.3 62.7 + - - +
421D THR* 4.2 17.1 - - + +
428D ALA* 4.0 19.9 - - + +
429D LEU 3.4 3.8 - - - +
430D MET* 3.9 27.7 - - + +
5E MAN 5.4 10.1 + - - -
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Residues in contact with VAL 420 (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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336D VAL* 5.1 2.5 - - + -
338D ALA* 4.8 5.8 - - + -
358D CYS* 4.6 1.6 - - - -
360D VAL* 3.7 34.8 - - + -
363D LEU* 6.2 1.1 - - + -
370D VAL* 4.8 8.5 - - + +
371D ASN 3.2 8.3 - - - +
372D LEU* 4.1 13.5 - - + +
418D CYS* 4.2 12.1 - - - +
419D ARG* 1.3 74.3 - - - +
421D THR* 1.3 73.0 + - - +
422D HIS* 5.2 2.0 - - + +
425D LEU* 6.1 2.5 - - + -
428D ALA* 4.0 0.3 - - - +
429D LEU* 2.8 55.4 + - + +
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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