Contacts of the helix formed by residues 668 - 680 (chain B) in PDB entry 3DXD
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 668 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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667B VAL* 1.3 75.6 - - - +
669B PRO* 1.4 81.6 - - + +
670B GLU* 3.4 35.4 + - - +
671B GLU* 3.4 21.3 + - + +
672B ARG* 3.1 27.4 + - - +
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Residues in contact with PRO 669 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667B VAL 4.8 0.4 - - - +
668B GLU* 1.4 100.4 - - + +
670B GLU* 1.3 65.2 + - - +
672B ARG* 3.4 4.4 + - + +
673B HIS* 3.1 26.4 + - - +
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Residues in contact with GLU 670 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641A PRO* 5.8 1.0 - - - +
642A ASN* 3.5 19.1 + - - +
644A ALA* 3.4 27.6 - - + +
645A SER* 4.9 4.3 + - - -
648A GLU* 4.2 18.4 - - - +
668B GLU* 3.4 25.4 + - - +
669B PRO* 1.3 77.2 - - - +
671B GLU* 1.3 58.3 + - - +
673B HIS* 4.0 1.4 - - - +
674B LEU* 3.0 35.2 + - + +
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Residues in contact with GLU 671 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667B VAL* 3.4 29.0 - - + +
668B GLU* 3.4 33.1 + - + +
669B PRO 3.2 0.6 - - - -
670B GLU* 1.3 79.1 - - - +
672B ARG* 1.3 64.5 + - - +
674B LEU* 3.3 11.6 - - - +
675B SER* 3.2 29.8 + - - +
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Residues in contact with ARG 672 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667B VAL* 3.4 49.3 + - + +
668B GLU 3.1 14.5 + - - +
669B PRO* 3.4 4.9 + - + +
671B GLU* 1.3 76.2 - - - +
673B HIS* 1.3 64.5 + - - +
675B SER* 3.4 6.9 + - - -
676B LYS* 3.2 48.2 + - + +
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Residues in contact with HIS 673 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648A GLU* 3.6 36.7 + - + +
651A GLN* 2.7 37.7 + - - -
655A MET* 6.0 0.2 - - - +
669B PRO 3.1 16.9 + - - +
670B GLU 4.0 3.1 - - - +
672B ARG* 1.3 76.9 - - - +
674B LEU* 1.3 56.3 + - - +
676B LYS* 3.5 20.9 + - + +
677B MET* 2.8 46.0 + - + +
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Residues in contact with LEU 674 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614A VAL* 3.9 27.1 - - + -
618A VAL* 3.7 33.0 - - + +
642A ASN* 4.2 11.9 - - - +
644A ALA* 3.9 31.0 - - + +
647A SER* 5.1 0.7 - - - +
648A GLU* 5.6 0.2 + - - -
670B GLU* 3.0 27.1 + - + +
671B GLU* 3.3 10.1 - - - +
673B HIS* 1.3 73.9 - - - +
675B SER* 1.3 61.5 + - - +
677B MET* 3.1 7.3 + - + +
678B GLN* 2.9 36.1 + - - +
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Residues in contact with SER 675 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671B GLU* 3.2 18.0 + - - +
672B ARG* 3.8 9.3 - - - -
673B HIS 3.4 0.2 - - - -
674B LEU* 1.3 74.2 - - - +
676B LYS* 1.3 61.3 + - - +
678B GLN* 3.2 12.8 + - - +
679B GLN* 2.9 51.8 + - - +
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Residues in contact with LYS 676 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672B ARG* 3.2 39.8 + - + +
673B HIS* 3.5 21.3 - - + +
675B SER* 1.3 79.3 - - - +
677B MET* 1.3 66.2 + - + +
679B GLN* 5.0 1.6 - - - +
680B ASN* 3.0 34.1 + - + +
681B GLY 3.4 5.1 + - - +
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Residues in contact with MET 677 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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612A LEU* 3.5 26.0 - - + -
613A ALA* 3.6 8.4 - - - +
614A VAL* 3.3 27.1 + - + -
647A SER* 3.8 25.6 - - - +
651A GLN* 3.5 27.4 - - - +
673B HIS* 2.8 31.7 + - + +
674B LEU* 3.1 12.3 + - + +
676B LYS* 1.3 74.7 - - + +
678B GLN* 1.3 57.0 + - - +
681B GLY* 3.1 28.5 + - - +
682B TYR* 3.8 22.7 - - + -
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Residues in contact with GLN 678 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559A VAL* 3.6 15.1 - - - +
563A ASN* 5.0 0.5 + - - -
614A VAL* 3.4 21.6 - - + +
615A GLY 2.8 29.2 + - - +
616A ARG* 3.0 42.7 + - - +
618A VAL* 3.9 24.9 - - - +
674B LEU* 2.9 22.4 + - - +
675B SER* 3.6 14.1 + - - +
677B MET* 1.3 76.8 - - - +
679B GLN* 1.3 63.1 + - + +
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Residues in contact with GLN 679 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559A VAL* 3.7 16.1 - - - +
616A ARG* 3.8 17.6 + - - +
675B SER* 2.9 37.1 + - - +
676B LYS* 4.4 1.3 - - - +
678B GLN* 1.3 76.3 - - + +
680B ASN* 1.3 76.2 + - - +
560C ASP* 6.1 1.3 - - - +
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Residues in contact with ASN 680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559A VAL* 3.7 7.5 - - - +
611A PHE* 3.6 15.2 - - - -
676B LYS* 3.0 16.5 + - + +
679B GLN* 1.3 96.2 + - - +
681B GLY* 1.3 69.0 + - - +
682B TYR* 4.6 0.2 - - - -
683B GLU* 5.9 0.2 - - - +
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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