Contacts of the helix formed by residues 635 - 650 (chain C) in PDB entry 3HZJ
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 PRO 635 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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556A ASP* 5.6 1.8 - - - +
561A LEU* 4.1 9.8 - - + -
565A ARG* 4.0 1.8 - - - +
635A PRO* 3.9 23.6 - - + -
637A GLU* 3.9 25.4 - - + +
638A GLN* 4.3 12.6 - - + +
906A UNX 3.8 9.9 - - - -
545C ALA* 5.8 2.0 - - + -
634C MSE 1.4 84.9 - - + +
636C GLU* 1.3 67.5 + - - +
637C GLU 4.6 0.4 - - - +
638C GLN* 3.0 33.8 + - - +
639C ALA* 2.9 19.4 + - - +
906C UNX 4.4 1.8 - - - -
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Residues in contact with GLU 636 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906A UNX 3.3 16.1 - - - -
564C TYR* 2.5 35.9 + - - +
568C ILE* 4.7 1.4 - - - +
601C GLU* 5.9 0.2 - - - +
602C SER* 2.7 35.3 + - - +
605C LYS* 3.3 28.6 + - - +
606C ILE* 3.4 21.7 - - + +
631C LEU* 3.7 13.0 - - - +
634C MSE 3.5 1.0 + - - -
635C PRO* 1.3 70.6 - - - +
637C GLU* 1.3 63.4 + - - +
639C ALA 3.2 2.8 + - - -
640C PHE* 3.1 17.2 + - - +
906C UNX 3.8 7.1 - - - -
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Residues in contact with GLU 637 (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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635A PRO* 3.9 10.3 - - + +
557C ASN 4.5 2.1 - - - +
560C MSE 3.7 1.9 - - - +
561C LEU* 3.2 47.2 + - + +
564C TYR* 3.5 40.6 - - + +
635C PRO 3.3 0.2 - - - -
636C GLU* 1.3 79.7 - - - +
638C GLN* 1.3 77.4 + - - +
640C PHE* 3.3 4.9 + - - +
641C CYS* 3.2 36.3 + - - -
906C UNX 3.2 16.7 - - - -
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Residues in contact with GLN 638 (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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556A ASP* 3.9 3.7 + - - +
635A PRO* 4.0 7.5 - - + +
638A GLN* 2.7 39.3 + - - +
545C ALA* 5.8 0.2 - - - +
549C GLN* 3.0 36.6 + - - +
556C ASP* 4.1 14.8 + - - +
634C MSE 3.4 13.4 - - + +
635C PRO* 3.0 28.3 + - + +
637C GLU* 1.3 88.4 + - - +
639C ALA* 1.3 57.5 + - - +
641C CYS* 3.2 8.5 + - - +
642C VAL* 3.0 31.7 + - - +
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Residues in contact with ALA 639 (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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606C ILE* 3.6 18.8 - - + -
627C ALA* 4.5 1.1 - - - +
630C LEU* 3.7 15.6 - - + +
631C LEU* 3.7 27.8 - - - +
634C MSE 3.6 10.4 - - - -
635C PRO 2.9 10.9 + - - +
636C GLU 3.2 9.6 + - - +
638C GLN* 1.3 73.8 - - - +
640C PHE* 1.3 59.3 + - - +
642C VAL 3.5 0.6 + - - +
643C LEU* 2.9 30.0 + - - +
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Residues in contact with PHE 640 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560C MSE 4.1 21.5 - - - -
564C TYR* 3.5 36.6 - + + -
567C LEU* 4.0 22.9 - - + -
606C ILE* 4.0 30.1 - - + +
609C ALA* 3.9 7.6 - - + -
610C TYR* 3.7 28.9 - + + -
613C TYR* 4.1 10.1 - + - -
636C GLU 3.1 9.3 + - - +
637C GLU 3.6 8.7 - - - +
638C GLN 3.3 0.2 - - - -
639C ALA* 1.3 73.2 - - - +
641C CYS* 1.3 73.8 + - - +
643C LEU* 3.1 4.8 + - + +
644C VAL* 2.9 49.1 + - + +
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Residues in contact with CYS 641 (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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554C CYS* 3.8 19.7 - - + -
557C ASN* 6.0 1.3 - - - -
560C MSE 3.4 26.7 - - + -
637C GLU* 3.2 38.1 + - - -
638C GLN* 3.2 10.8 + - + +
640C PHE* 1.3 82.3 - - - +
642C VAL* 1.3 64.0 + - - +
644C VAL* 3.2 7.9 + - - +
645C LYS* 3.0 24.8 + - - +
907C UNX 3.9 10.5 - - - -
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Residues in contact with VAL 642 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548C TRP* 4.6 5.2 - - + +
549C GLN* 3.9 23.3 - - + -
552C ALA* 4.5 11.0 - - + -
554C CYS* 4.2 12.6 - - - -
630C LEU* 3.6 28.3 - - + -
634C MSE 3.5 20.9 - - + -
638C GLN 3.0 20.2 + - - +
639C ALA 3.9 3.6 - - - +
641C CYS* 1.3 76.1 - - - +
643C LEU* 1.3 63.1 + - - +
645C LYS* 3.1 5.1 + - - +
646C ILE* 2.9 33.6 + - + +
721C LEU* 5.0 5.6 - - + -
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Residues in contact with LEU 643 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606C ILE* 3.8 26.0 - - + -
607C CYS* 5.6 1.1 - - - +
610C TYR* 4.3 18.2 - - + -
623C GLN* 3.7 35.7 - - + +
626C LEU* 3.6 33.9 - - + -
627C ALA* 4.3 12.3 - - + +
630C LEU* 3.7 11.2 - - + +
639C ALA 2.9 18.3 + - - +
640C PHE* 3.1 5.3 + - + +
642C VAL* 1.3 77.4 - - - +
644C VAL* 1.3 57.6 + - - +
646C ILE* 3.2 3.5 + - - +
647C MSE 2.9 37.8 + - + +
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Residues in contact with VAL 644 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560C MSE 6.0 3.1 - - - -
610C TYR* 4.1 15.5 - - + -
613C TYR* 3.7 36.1 - - + +
640C PHE* 2.9 51.1 + - + +
641C CYS* 3.2 9.8 + - - +
643C LEU* 1.3 75.3 - - - +
645C LYS* 1.3 64.6 + - + +
647C MSE 3.2 5.1 + - - +
648C TYR* 2.9 38.2 + - + +
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Residues in contact with LYS 645 (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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552C ALA* 3.3 36.1 + - + +
553C GLY* 4.1 14.3 + - - -
554C CYS* 3.9 10.8 - - - -
641C CYS 3.0 17.7 + - - +
642C VAL 3.5 7.2 - - - +
644C VAL* 1.3 79.5 - - + +
646C ILE* 1.3 58.9 + - - +
648C TYR* 5.2 0.4 - - + -
649C ASP* 2.8 61.8 + - + +
650C TYR* 3.2 7.5 + - + -
907C UNX 4.5 12.1 - - - -
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Residues in contact with ILE 646 (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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626C LEU* 4.1 20.9 - - + -
630C LEU* 4.2 20.2 - - + -
642C VAL* 2.9 35.1 + - + +
643C LEU* 3.7 5.2 - - - +
645C LYS* 1.3 76.9 - - + +
647C MSE 1.3 64.5 + - - +
650C TYR* 3.5 22.4 + - + +
652C LEU* 3.5 33.7 + - + -
703C LEU* 4.3 0.7 - - + -
717C ILE* 4.9 4.9 - - + -
720C LEU* 4.1 23.3 - - + -
721C LEU* 4.0 26.0 - - + -
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Residues in contact with MSE 647 (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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610C TYR* 3.2 40.8 - - + +
617C ILE* 4.4 0.7 - - + -
620C CYS* 4.2 13.0 - - - -
623C GLN* 3.7 23.3 - - - +
626C LEU* 4.9 0.7 - - - -
643C LEU* 2.9 28.9 + - + +
644C VAL 3.8 2.9 - - - +
646C ILE* 1.3 76.9 - - - +
648C TYR* 1.3 65.0 + - + +
651C GLY 4.0 0.7 - - - -
652C LEU* 3.4 30.2 + - - -
653C ARG* 3.0 58.4 + - + +
656C TYR* 3.9 19.7 - - + -
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Residues in contact with TYR 648 (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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610C TYR* 3.7 19.5 - + - -
613C TYR* 3.8 28.2 + + - -
614C ASP* 3.2 33.1 + - - +
615C GLU 4.8 0.2 + - - -
644C VAL* 2.9 32.4 + - + +
647C MSE 1.3 80.2 - - + +
649C ASP* 1.3 71.3 + - - +
650C TYR 3.5 0.4 - - - -
651C GLY* 3.7 7.6 + - - -
653C ARG* 3.4 35.3 + - - +
654C ASP* 5.2 3.3 - - - +
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Residues in contact with ASP 649 (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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552C ALA 4.5 3.4 - - - +
645C LYS* 2.8 56.6 + - + +
648C TYR* 1.3 81.3 - - - +
650C TYR* 1.3 66.1 + - + -
651C GLY 3.3 2.6 + - - -
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Residues in contact with TYR 650 (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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527C ARG* 5.1 1.2 + - - -
551C LEU 3.1 20.4 + - - -
552C ALA* 4.4 13.9 - - + -
645C LYS* 3.2 18.3 + - + -
646C ILE* 3.5 23.1 + - + +
649C ASP* 1.3 84.1 - - + +
651C GLY* 1.3 62.2 + - - +
652C LEU* 3.4 3.1 + - + +
720C LEU* 3.4 29.4 - - + -
721C LEU* 2.5 50.5 + - + -
724C GLY* 4.3 13.9 - - - -
725C LEU* 3.6 22.7 + - - +
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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