Contacts of the strand formed by residues 434 - 450 (chain A) in PDB entry 1FCP
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 434 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385A ASN 3.9 0.7 - - - +
386A ASP* 3.8 2.6 - - - +
387A ILE* 2.8 46.0 + - + +
432A TYR* 3.4 43.9 - - + +
433A ARG* 1.3 76.2 - - - +
435A LEU* 1.3 63.3 + - - +
436A ASN* 3.4 16.6 - - - +
469A SER* 3.1 26.5 - - - +
470A LEU 3.1 6.5 - - - +
471A ASN* 3.2 42.8 - - + +
472A ARG* 4.5 3.1 - - - +
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Residues in contact with LEU 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384A ARG* 3.9 30.5 - - + +
385A ASN 3.7 5.6 - - - +
386A ASP* 3.2 41.1 - - + +
434A ILE* 1.3 74.2 - - - +
436A ASN* 1.3 65.4 + - - +
437A LYS* 4.2 17.1 - - + +
468A GLU 3.6 1.9 - - - +
469A SER* 3.4 3.5 - - - -
470A LEU* 2.7 49.7 + - + +
472A ARG* 4.0 19.7 - - - +
3B KDO 3.7 6.1 - - - +
4B GMH 4.3 10.5 - - - +
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Residues in contact with ASN 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A ASN* 2.8 40.4 + - - +
115A PHE* 5.9 0.7 - - - -
383A MSE 4.0 2.8 - - - +
384A ARG* 3.4 4.5 - - - +
385A ASN* 2.9 40.2 + - + +
387A ILE* 4.2 6.9 - - - +
434A ILE* 3.4 10.4 - - - +
435A LEU* 1.3 73.4 - - - +
437A LYS* 1.3 64.0 + - - +
438A GLN* 5.2 5.8 - - - +
468A GLU 3.8 1.1 + - - -
469A SER* 2.9 34.2 + - - -
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Residues in contact with LYS 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383A MSE 3.4 5.6 - - - +
384A ARG* 3.0 41.6 - - + +
435A LEU* 4.2 15.3 - - + +
436A ASN* 1.3 79.2 - - - +
438A GLN* 1.3 72.9 + - - +
439A LYS* 6.3 0.7 - - + -
467A GLN* 3.6 3.1 - - - +
468A GLU* 2.9 61.0 + - + +
1B GP1 3.0 30.9 + - - +
4B GMH 5.6 2.2 + - - -
9B KDO 5.4 0.8 + - - -
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Residues in contact with GLN 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A GLN* 3.3 12.7 - - - +
113A GLY 4.9 0.4 + - - -
114A ASN* 4.4 13.3 - - - +
142A LYS* 2.4 34.8 + - - +
381A MSE 4.4 4.0 - - - -
382A ARG* 3.2 5.1 - - - +
383A MSE 2.8 70.4 + - + +
436A ASN* 5.2 3.6 - - - +
437A LYS* 1.3 85.2 - - - +
439A LYS* 1.3 65.8 + - - +
466A ASP 3.6 6.7 - - - +
467A GLN* 4.5 10.8 - - + -
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Residues in contact with LYS 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A LYS* 5.6 2.7 + - - +
380A PHE* 4.8 11.4 - - + -
381A MSE 3.4 9.9 - - - +
382A ARG* 4.2 15.0 - - + +
437A LYS* 6.3 0.7 - - + -
438A GLN* 1.3 80.8 - - - +
440A GLN* 1.3 61.6 + - - +
441A THR* 6.0 0.2 - - - +
464A TRP 4.0 1.1 - - - -
465A ALA* 3.5 1.4 - - - -
466A ASP* 2.8 54.0 + - + +
906A LIM 4.0 17.3 + - - +
1012A NI 3.3 35.3 - - - +
1B GP1 4.4 2.7 - - - -
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Residues in contact with GLN 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A TYR* 5.6 0.2 + - - -
140A TYR 3.4 9.1 + - - -
141A GLY* 3.2 11.3 - - - -
142A LYS* 2.9 58.7 + - - +
379A ASP* 3.7 3.4 + - - +
380A PHE* 3.3 5.4 - - - -
381A MSE 3.0 50.6 + - + +
439A LYS* 1.3 76.6 - - - +
441A THR* 1.3 63.5 + - - +
461A ARG* 3.6 6.4 - - - +
463A ASP* 3.3 22.2 - - - +
464A TRP 3.2 7.6 - - - +
465A ALA* 4.2 6.1 - - - +
509A PHE* 3.6 8.8 - - - -
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Residues in contact with THR 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378A VAL* 5.7 4.5 - - + -
379A ASP 3.1 7.6 - - - +
380A PHE* 3.3 26.7 - - + -
439A LYS* 6.0 0.2 - - - +
440A GLN* 1.3 74.5 - - - +
442A GLY* 1.3 66.7 + - - +
443A VAL* 5.5 2.9 - - + -
463A ASP* 3.3 4.9 - - - -
464A TRP* 2.8 57.5 + - + -
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Residues in contact with GLY 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377A GLY 4.5 0.2 - - - -
378A VAL* 3.0 10.4 - - - +
379A ASP 2.7 40.2 + - - -
441A THR* 1.3 77.5 - - - +
443A VAL* 1.3 64.2 + - - +
444A TYR* 4.1 1.8 - - - -
461A ARG* 3.8 12.2 - - - +
462A TYR 3.2 8.7 - - - -
463A ASP* 3.7 11.1 + - - -
464A TRP* 5.0 0.4 - - - -
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Residues in contact with VAL 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A GLY 3.5 5.4 - - - +
378A VAL* 3.9 19.1 - - + -
441A THR* 5.5 3.6 - - + -
442A GLY* 1.3 78.6 - - - +
444A TYR* 1.3 59.9 + - - +
445A VAL* 5.4 3.1 - - + -
461A ARG* 3.2 2.4 - - - +
462A TYR* 2.9 43.7 + - + +
464A TRP* 4.1 19.7 - - + -
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Residues in contact with TYR 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LYS* 3.9 18.1 - - + +
138A VAL 3.8 7.0 - - - +
139A LEU* 3.8 18.6 - - + -
358A ASP* 2.6 37.6 + - - -
359A THR 4.0 0.2 + - - -
360A GLN* 3.0 16.1 + - - +
375A LEU* 4.1 20.0 - - + -
376A THR* 3.5 1.6 - - - -
377A GLY* 3.0 54.4 + - - -
378A VAL 4.0 0.7 - - - -
379A ASP* 4.1 11.9 - - + -
442A GLY 4.4 1.8 - - - -
443A VAL* 1.3 78.1 - - - +
445A VAL* 1.3 71.9 + - - +
460A GLY 3.2 12.3 - - - +
461A ARG* 3.4 31.0 - - + -
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Residues in contact with VAL 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A LEU* 3.7 24.0 - - + -
375A LEU 3.2 3.1 - - - -
376A THR* 3.9 15.9 - - + -
443A VAL* 5.4 1.8 - - + -
444A TYR* 1.3 82.8 - - - +
446A GLN* 1.3 64.2 + - - +
459A GLY* 3.1 3.5 - - - -
460A GLY 2.8 31.9 + - - +
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Residues in contact with GLN 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A THR* 2.7 40.4 + - - -
39A THR* 4.6 0.2 + - - -
138A VAL* 5.0 2.7 - - + +
139A LEU* 3.8 18.6 - - + +
373A THR 3.8 0.2 - - - +
374A LEU* 3.3 5.8 - - - +
375A LEU* 2.5 55.8 + - + +
444A TYR* 5.5 0.2 - - - -
445A VAL* 1.3 78.0 - - - +
447A ASP* 1.3 69.5 + - - +
448A GLN* 4.2 9.7 + - + +
457A THR* 4.1 11.0 - - + +
458A LEU 3.5 13.9 - - - +
459A GLY* 4.2 4.5 - - - -
488A ARG* 2.8 30.3 + - - -
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Residues in contact with ASP 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A HIS* 3.4 20.1 + - - +
373A THR 3.2 28.2 + - - -
374A LEU* 3.4 16.5 + - + +
446A GLN* 1.3 75.8 - - - +
448A GLN* 1.3 65.0 + - - +
449A ALA* 3.2 29.6 + - - +
456A VAL 3.7 2.4 - - - +
457A THR* 3.6 5.9 - - - +
458A LEU* 3.0 31.8 + - + +
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Residues in contact with GLN 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A THR* 3.5 24.2 + - - +
39A THR* 2.5 24.7 + - - +
41A THR* 3.0 29.8 + - - +
45A LYS 4.9 4.0 + - - -
371A ASP 3.5 3.6 - - - +
373A THR* 2.7 57.2 + - - +
446A GLN* 4.2 12.1 + - - +
447A ASP* 1.3 77.1 - - - +
449A ALA* 1.3 60.2 + - - +
450A GLN* 3.9 0.9 + - - +
455A LEU* 4.3 16.3 - - + +
456A VAL 3.9 3.8 - - - -
457A THR* 4.3 11.9 + - + +
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Residues in contact with ALA 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A ILE* 4.0 9.4 - - + -
371A ASP 3.2 5.2 - - - -
372A HIS* 3.8 18.8 - - + +
447A ASP* 3.2 17.9 + - - +
448A GLN* 1.3 73.2 - - - +
450A GLN* 1.3 59.7 + - - +
451A TRP* 5.7 0.2 - - - -
455A LEU* 3.3 1.6 - - - +
456A VAL* 2.7 54.0 + - + +
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Residues in contact with GLN 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LYS* 3.1 34.8 + - - +
369A ASP 3.6 3.1 - - - +
370A ILE* 4.8 1.3 - - - -
371A ASP* 2.9 39.6 + - + +
448A GLN 3.9 0.6 + - - +
449A ALA* 1.3 73.4 - - - +
451A TRP* 1.3 60.3 - - - +
452A ASP* 3.4 11.8 + - - +
453A LYS* 3.8 23.8 - - - +
454A VAL 3.5 9.2 - - - +
455A LEU* 3.5 23.1 - - + +
494A LEU* 4.3 14.2 - - - +
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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