Contacts of the strand formed by residues 631 - 638 (chain C) in PDB entry 3DXE
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 SER 631 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626C ALA* 3.4 2.9 - - - -
627C ALA* 2.7 38.9 + - - +
628C GLY* 3.3 23.5 + - - +
629C PRO 3.7 0.4 + - - -
630C ALA* 1.3 78.7 - - - +
632C PHE* 1.3 61.3 + - - +
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Residues in contact with PHE 632 (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 PRO* 3.4 8.3 - - - +
553C VAL* 3.0 46.8 + - + +
554C ALA 4.0 13.0 - - - -
555C LYS 3.9 15.7 - - - +
556C PRO* 3.6 41.3 - - + -
610C SER* 4.7 0.7 - - - -
624C ILE* 3.9 2.0 - - + -
625C MET 3.3 4.5 - - - +
626C ALA* 3.7 25.8 - - + -
627C ALA* 5.2 0.7 - - - -
628C GLY 5.1 0.7 - - - -
629C PRO 4.6 8.7 - - - -
630C ALA* 4.3 7.2 - - - -
631C SER* 1.3 88.2 + - - +
633C CYS* 1.3 60.8 + - - +
687D TYR* 3.7 18.6 - + - -
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Residues in contact with CYS 633 (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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550C ASN* 3.6 28.3 - - - -
551C VAL 3.5 7.4 - - - -
552C PRO* 4.4 1.1 - - + -
553C VAL* 4.3 3.6 - - - -
623C PHE 3.9 0.5 - - - +
624C ILE* 3.4 1.0 - - - -
625C MET* 2.8 43.9 + - + +
627C ALA* 4.4 15.9 - - + -
632C PHE* 1.3 75.7 - - - +
634C CYS* 1.3 62.7 + - - +
635C HIS* 3.6 24.6 + - - +
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Residues in contact with CYS 634 (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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549C GLY 3.8 0.5 - - - +
550C ASN* 3.0 5.1 - - - -
551C VAL* 2.6 38.8 + - + +
553C VAL* 3.6 28.0 - - + +
562C ILE* 4.2 13.9 - - - -
565C ALA* 3.9 15.3 - - - -
622C ALA* 3.7 29.2 - - - -
623C PHE 3.5 7.2 - - - +
624C ILE* 4.3 3.1 - - + +
633C CYS* 1.3 73.8 - - - +
635C HIS* 1.3 60.8 + - - +
636C MET* 3.8 14.5 - - - +
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Residues in contact with HIS 635 (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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547C TYR* 2.7 29.1 + - + -
549C GLY 3.7 3.4 - - - -
550C ASN* 3.6 15.6 - - + +
592C ILE* 4.0 7.6 - - + +
602C GLY* 5.6 5.6 - - - -
604C CYS* 3.9 16.7 - - - -
622C ALA* 3.1 5.5 - - - +
623C PHE* 2.9 69.9 + + + -
625C MET* 3.8 13.6 - - + +
633C CYS* 3.6 18.7 - - - +
634C CYS* 1.3 76.8 - - - +
636C MET* 1.3 59.7 + - - +
637C PHE* 3.9 8.7 - - + -
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Residues in contact with MET 636 (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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547C TYR* 3.3 10.8 - - - -
548C LEU* 2.8 36.6 + - + +
549C GLY 3.0 28.3 + - - +
551C VAL* 3.8 28.3 - - + -
565C ALA* 3.6 36.6 - - - +
566C LEU* 3.7 21.8 - - + -
569C VAL* 3.8 26.5 - - + -
621C PHE 3.4 4.3 - - - -
622C ALA* 3.9 3.6 - - + -
634C CYS* 3.8 15.5 - - - +
635C HIS* 1.3 78.5 - - - +
637C PHE* 1.3 60.1 + - - +
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Residues in contact with PHE 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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545C VAL* 3.8 20.2 - - + -
546C TYR 3.1 9.6 - - - +
547C TYR* 3.4 26.9 - + + -
548C LEU* 3.8 11.0 - - - +
583C VAL* 3.7 22.0 - - + -
592C ILE* 3.6 33.2 - - + -
620C THR* 3.4 6.4 - - - -
621C PHE* 2.9 51.5 + + + +
623C PHE* 3.4 29.4 - + - -
635C HIS 3.9 13.2 - - - -
636C MET* 1.3 74.7 - - - +
638C TRP* 1.3 59.5 + - - +
639C CYS* 4.2 16.6 - - - -
646C LEU* 4.3 4.9 - - + -
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Residues in contact with TRP 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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571A SER* 3.3 32.8 - - - -
545C VAL* 3.5 3.5 - - - +
546C TYR* 2.9 47.3 + + + -
548C LEU* 3.9 7.3 - - + +
570C LEU* 4.6 8.5 - - + -
575C ARG* 3.6 23.5 - - - +
578C TRP* 3.4 37.7 - + + -
617C ASP* 3.5 21.1 - - - -
619C HIS* 3.3 33.2 - + + -
620C THR* 3.8 30.1 - - + -
637C PHE* 1.3 73.4 - - - +
639C CYS* 1.3 62.6 + - - +
640C GLU* 2.9 32.7 + - + -
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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
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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