Contacts of the helix formed by residues 503 - 518 (chain A) in PDB entry 1FGR
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 503 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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498A SER 3.8 14.1 - - - +
499A HIS* 2.6 20.7 + - - -
502A ASN* 1.3 83.4 - - - +
504A HIS* 1.3 81.4 + - - +
505A ALA 3.5 0.2 - - - -
507A MET* 3.0 28.2 + - - +
685A ILE* 4.0 9.4 - - - +
689A LEU* 4.2 12.3 - - + -
690A HIS* 3.5 36.3 - - + +
693A VAL* 4.5 2.9 - - + -
837A ILE* 3.3 19.1 - - - -
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Residues in contact with HIS 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A HIS* 3.1 17.4 + + - -
500A TRP* 3.4 30.5 + + + +
503A THR* 1.3 93.0 + - - +
505A ALA* 1.3 63.8 + - - +
507A MET* 4.2 0.2 - - - +
508A GLU 3.5 10.0 + - - -
535A ASN* 3.8 3.9 + - - +
538A ILE* 2.9 30.7 - - + +
539A ASN* 2.9 27.8 + - - +
837A ILE* 3.3 23.4 - - + +
839A ILE* 3.5 12.3 - - - -
840A FE 2.1 32.6 - - - -
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Residues in contact with ALA 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A TYR* 4.0 16.3 + - - +
214A TYR* 4.6 4.7 - - + +
215A PRO* 3.4 21.3 - - + +
216A ARG 4.5 1.0 - - - +
500A TRP* 2.9 41.5 + - + +
501A LEU* 3.7 11.4 - - + +
504A HIS* 1.3 71.9 - - - +
506A ALA* 1.3 66.2 + - - +
507A MET 3.3 0.2 + - - -
508A GLU* 3.6 2.6 + - - +
509A PRO* 3.1 19.6 - - - +
539A ASN* 4.5 1.3 - - - +
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Residues in contact with ALA 506 (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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215A PRO* 4.4 3.1 - - + -
501A LEU* 2.9 20.5 + - + +
502A ASN 3.6 17.5 - - - +
503A THR 3.5 0.6 + - - -
505A ALA* 1.3 77.1 - - - +
507A MET* 1.3 61.3 + - - +
509A PRO* 3.4 2.4 - - - +
510A PHE* 3.5 10.1 - - + -
571A TYR* 6.1 0.4 - - + -
574A TRP* 4.1 29.2 - - + +
657A HIS* 2.9 31.2 + - + -
685A ILE* 5.5 4.9 - - + -
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Residues in contact with MET 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A THR 3.0 18.8 + - - +
504A HIS 4.2 0.4 - - - +
506A ALA* 1.3 77.2 - - - +
508A GLU* 1.3 65.5 + - - +
509A PRO 3.3 0.2 - - - -
510A PHE* 3.0 25.4 + - + +
511A VAL* 3.2 12.9 + - + +
531A HIS 5.0 0.2 - - - +
532A TYR* 3.9 17.7 - - + -
535A ASN* 3.1 24.2 - - - +
682A ILE* 3.4 46.9 - - + +
685A ILE* 3.6 30.5 - - + -
686A ALA* 3.8 11.4 - - + +
837A ILE* 3.7 5.2 - - + -
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Residues in contact with GLU 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A TYR* 4.1 3.4 + - - +
216A ARG 4.3 2.9 - - - +
217A ARG* 3.8 14.3 - - - +
218A GLY* 2.8 31.5 + - - -
504A HIS 3.5 5.3 + - - +
505A ALA* 4.1 3.4 - - - +
507A MET* 1.3 77.9 - - - +
509A PRO* 1.3 69.2 - - + +
511A VAL* 3.0 18.3 + - - +
512A ILE* 3.1 22.7 + - + +
535A ASN* 4.5 2.9 + - - +
536A MET* 3.7 28.8 - - + +
539A ASN* 2.8 40.4 + - - +
543A ARG* 4.1 6.4 + - - -
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Residues in contact with PRO 509 (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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186A TYR* 3.8 14.2 - - + -
215A PRO* 4.0 1.6 - - + -
216A ARG 3.4 20.9 - - - +
505A ALA 3.1 17.3 - - - +
506A ALA 3.4 8.3 - - - +
508A GLU* 1.3 92.9 - - + +
510A PHE* 1.3 57.2 + - + +
512A ILE* 3.5 1.7 + - + -
513A ALA* 3.0 28.9 + - - +
652A ALA* 4.7 2.9 - - - +
656A GLY* 3.4 37.2 - - - +
657A HIS* 3.8 19.7 - - + +
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Residues in contact with PHE 510 (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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506A ALA* 3.5 27.1 - - + -
507A MET* 3.0 27.3 + - + +
509A PRO* 1.3 74.5 - - - +
511A VAL* 1.3 60.6 + - - +
513A ALA* 4.0 4.0 - - - +
514A THR* 2.7 35.1 + - - -
532A TYR* 4.1 12.3 - - - +
574A TRP* 4.9 2.7 - + - -
576A PHE* 3.7 33.4 - + - -
648A TRP* 4.2 4.4 + + - +
649A TRP* 3.7 25.8 - + - -
652A ALA* 3.9 21.1 - - + -
657A HIS* 3.7 21.8 - + - -
666A TRP* 4.5 7.6 - + - -
682A ILE* 4.0 20.4 - - + -
685A ILE* 5.8 2.7 - - + -
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Residues in contact with VAL 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A GLU* 4.6 5.8 - - - +
507A MET* 3.2 13.8 + - + +
508A GLU* 3.0 13.0 + - - +
510A PHE* 1.3 77.2 - - - +
512A ILE* 1.3 65.0 + - - +
514A THR* 3.5 1.0 - - - -
515A HIS* 3.2 40.2 + - + +
532A TYR* 3.6 49.4 - - + +
535A ASN* 4.2 16.6 - - + +
536A MET* 3.8 29.6 - - + -
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Residues in contact with ILE 512 (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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184A TYR* 4.1 10.3 - - + +
185A ASP 3.7 21.3 - - - +
186A TYR* 3.5 30.5 - - + -
217A ARG* 3.6 10.1 - - - +
218A GLY* 3.6 32.3 - - - +
508A GLU* 3.1 21.2 + - + +
509A PRO* 3.8 2.2 - - + +
511A VAL* 1.3 76.7 - - - +
513A ALA* 1.3 62.8 + - - +
515A HIS* 3.2 4.7 + - - +
516A ARG* 3.0 44.7 + - - +
536A MET* 4.0 20.4 - - + -
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Residues in contact with ALA 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A TYR* 3.3 20.1 + - - +
509A PRO 3.0 17.1 + - - +
510A PHE 4.0 3.1 - - - +
512A ILE* 1.3 75.3 - - - +
514A THR* 1.3 56.6 + - - +
516A ARG* 3.3 0.5 + - - +
517A HIS* 2.9 29.6 + - - +
648A TRP* 3.4 26.8 - - + +
651A GLU* 3.9 6.7 - - + +
652A ALA* 3.8 21.8 - - + +
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Residues in contact with THR 514 (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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510A PHE 2.7 22.9 + - - -
511A VAL 3.5 4.9 - - - -
512A ILE 3.2 0.2 - - - -
513A ALA* 1.3 77.2 - - - +
515A HIS* 1.3 58.1 + - + +
518A LEU* 2.9 45.2 + - + +
525A TYR* 3.8 24.2 - - + -
528A LEU* 4.8 3.3 - - + +
529A THR* 3.9 8.3 - - + -
532A TYR* 2.8 32.7 + - + +
648A TRP* 3.2 19.3 + - - -
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Residues in contact with HIS 515 (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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166A LEU* 3.6 7.1 - - - +
169A LEU* 3.6 29.5 - - + +
184A TYR* 3.4 55.8 + + + -
244A GLU* 3.3 14.4 + - - -
511A VAL* 3.2 29.9 + - + +
512A ILE 3.2 3.0 + - - +
514A THR* 1.3 84.3 - - - +
516A ARG* 1.3 62.0 + - - +
517A HIS 3.6 0.3 + - - -
518A LEU 4.3 1.2 - - - +
525A TYR* 3.2 38.5 + + - -
529A THR* 4.4 11.2 - - + +
532A TYR* 4.7 3.8 - + - +
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Residues in contact with ARG 516 (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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166A LEU* 3.7 6.7 - - - +
169A LEU* 5.0 2.9 - - - -
170A ARG* 3.0 78.2 + - + +
184A TYR* 2.8 48.5 + - + +
185A ASP* 3.5 20.0 + - - -
186A TYR* 3.9 5.9 - - - -
512A ILE* 3.0 33.0 + - - +
513A ALA 3.8 0.9 - - - +
514A THR 3.3 0.4 - - - -
515A HIS* 1.3 79.3 - - - +
517A HIS* 1.3 58.5 + - + +
651A GLU* 2.9 44.3 + - - +
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Residues in contact with HIS 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A LEU* 3.7 7.4 - - - +
170A ARG* 3.7 30.7 + - - -
513A ALA 2.9 14.3 + - - +
516A ARG* 1.3 81.5 + - + +
518A LEU* 1.3 60.2 + - - +
519A SER 4.0 0.2 - - - -
644A GLU* 3.2 31.9 - - - +
647A HIS* 3.6 34.8 - + + +
648A TRP* 3.7 24.0 - - - +
651A GLU* 2.8 45.4 + - + +
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Residues in contact with LEU 518 (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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166A LEU* 3.8 7.2 - - - +
169A LEU* 5.9 0.2 - - - +
514A THR* 2.9 29.4 + - + +
515A HIS 4.3 1.4 - - - +
517A HIS* 1.3 82.2 - - - +
519A SER* 1.3 64.0 + - - +
520A VAL 3.7 0.3 + - - -
522A HIS* 4.1 12.3 - - + +
524A ILE* 3.8 30.5 - - + -
525A TYR* 3.2 31.3 - - + +
528A LEU* 5.4 0.2 - - + -
644A GLU* 3.6 20.0 - - + +
645A LEU* 3.9 7.6 - - + +
648A TRP* 3.7 44.6 - - + +
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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
------------------------------------------------------------
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