Contacts of the helix formed by residues 498 - 508 (chain C) in PDB entry 3MGH
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 GLU 498 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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494C VAL* 4.4 13.2 - - + +
495C PRO* 2.9 37.7 + - + +
497C SER* 1.3 83.2 + - - +
499C PHE* 1.3 59.9 + - - +
500C ALA 3.4 1.8 - - - -
501C CYS* 3.2 5.4 + - - +
502C ALA* 2.8 30.1 + - - +
529C GLU 4.6 1.7 - - - +
530C HIS* 2.9 62.8 + - - +
531C ALA* 5.4 0.7 - - + -
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Residues in contact with PHE 499 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411C LEU* 4.1 21.3 - - + -
413C VAL* 4.1 22.0 - - + -
431C LEU* 3.6 32.8 - - + -
433C THR* 3.6 27.4 - - + -
494C VAL* 4.4 2.5 - - + -
495C PRO 3.6 3.3 + - - -
496C TYR* 3.0 38.8 + + + +
497C SER 3.3 0.2 - - - -
498C GLU* 1.3 77.4 - - - +
500C ALA* 1.3 65.2 + - - +
502C ALA* 3.1 3.8 + - - -
503C LEU* 2.8 51.1 + - + +
554C PRO 5.2 6.7 - - - +
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Residues in contact with ALA 500 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496C TYR 4.9 0.2 + - - -
497C SER 5.3 0.2 - - - -
498C GLU 3.4 0.4 - - - -
499C PHE* 1.3 78.0 - - - +
501C CYS* 1.3 58.9 + - - +
503C LEU* 3.4 10.2 + - - +
504C LEU* 3.0 29.2 + - - +
553C THR* 3.1 29.2 + - - +
554C PRO 3.6 8.6 + - - +
555C THR* 3.2 32.1 - - - +
556C GLU* 3.6 9.7 - - - +
559C VAL* 4.6 3.8 - - + -
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Residues in contact with CYS 501 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497C SER 5.7 0.6 + - - -
498C GLU* 3.2 4.9 + - - +
500C ALA* 1.3 78.9 - - - +
502C ALA* 1.3 57.6 + - - +
504C LEU* 3.5 7.7 + - - +
505C TYR* 3.1 28.8 + - - +
527C LEU* 4.1 7.1 - - + +
528C SER 3.7 5.6 - - - +
529C GLU* 3.3 14.5 - - - +
530C HIS 3.8 4.9 - - - +
531C ALA* 3.4 34.1 - - - +
532C LEU 3.5 10.8 - - - -
553C THR* 3.6 19.1 - - - -
559C VAL* 3.9 15.9 - - - -
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Residues in contact with ALA 502 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C LEU* 3.7 28.7 - - + -
494C VAL* 3.9 17.7 - - + -
498C GLU 2.8 20.1 + - - +
499C PHE 3.7 2.9 - - - +
501C CYS* 1.3 69.9 - - - +
503C LEU* 1.3 61.3 + - - +
505C TYR* 3.2 0.6 + - - -
506C PHE* 2.9 45.7 + - + +
529C GLU 3.2 13.4 + - - +
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Residues in contact with LEU 503 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413C VAL* 4.1 16.2 - - + -
415C CYS* 4.0 14.4 - - - -
419C ARG* 3.9 30.7 - - - +
431C LEU* 3.4 19.4 - - + +
499C PHE* 2.8 47.4 + - + +
500C ALA* 3.4 8.7 - - - +
502C ALA* 1.3 76.9 - - - +
504C LEU* 1.3 62.8 + - - +
506C PHE 4.0 0.3 - - - -
507C THR* 2.8 30.8 + - - -
556C GLU* 3.6 15.5 - - + +
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Residues in contact with LEU 504 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500C ALA 3.0 16.1 + - - +
501C CYS* 3.7 6.1 - - - +
502C ALA 3.3 0.2 - - - -
503C LEU* 1.3 76.9 - - - +
505C TYR* 1.3 62.4 + - - +
507C THR* 3.8 2.1 - - - +
508C GLY* 3.1 19.1 + - - +
512C PHE* 4.1 16.6 - - + -
513C ASN* 3.5 8.4 - - - +
516C MET* 4.0 7.6 - - + -
527C LEU* 4.0 18.8 - - + -
556C GLU* 3.3 13.2 + - + +
559C VAL* 3.6 39.0 - - + -
560C PHE* 3.8 22.2 - - + -
573C ARG* 3.4 24.2 + - - +
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Residues in contact with TYR 505 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501C CYS 3.1 19.1 + - - +
502C ALA 3.9 1.1 - - - +
504C LEU* 1.3 78.8 - - + +
506C PHE* 1.3 90.2 + + - +
508C GLY* 3.3 4.2 + - - -
513C ASN* 2.9 43.6 + - + -
517C ARG* 4.2 9.2 - - - -
528C SER* 4.5 3.8 - - - -
529C GLU* 3.5 46.3 + - + +
5E A 3.1 39.8 + + - -
6E G 3.8 1.9 + - - -
6F C 3.4 31.3 + - + +
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Residues in contact with PHE 506 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415C CYS* 3.4 18.2 - - + +
416C GLY* 2.8 22.0 + - - -
429C ASP* 4.5 15.7 - - + +
431C LEU* 4.6 8.3 - - + -
472C LYS* 4.3 6.5 - - + -
492C ILE* 3.9 43.7 - - + -
494C VAL* 5.3 1.3 - - + -
502C ALA* 2.9 37.5 + - + +
505C TYR* 1.3 96.9 - + - +
507C THR* 1.3 60.0 + - - +
508C GLY* 3.3 0.4 - - - -
529C GLU* 3.7 30.1 - - + -
6F C 3.3 28.7 - - + -
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Residues in contact with THR 507 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415C CYS* 3.7 5.2 - - - +
416C GLY* 3.5 9.7 - - - +
419C ARG* 2.8 45.2 + - + +
420C ARG* 2.8 43.8 + - + +
503C LEU 2.8 23.0 + - - -
504C LEU 3.8 3.1 - - - -
506C PHE* 1.3 79.5 - - - +
508C GLY* 1.3 69.2 + - - +
570C PRO* 4.4 5.4 - - + -
573C ARG* 3.9 10.8 - - - +
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Residues in contact with GLY 508 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420C ARG* 3.6 1.1 - - - -
504C LEU 3.1 9.4 + - - +
505C TYR 3.3 12.9 + - - -
506C PHE 4.6 0.2 - - - -
507C THR* 1.3 87.9 - - - +
509C SER* 1.3 72.4 + - - -
512C PHE* 3.8 9.7 - - - -
513C ASN* 3.7 7.0 - - - -
573C ARG* 3.5 22.1 - - - +
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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