Contacts of the helix formed by residues 668 - 680 (chain D) 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 ALA 668 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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667D VAL* 1.3 74.9 - - - +
669D PRO* 1.4 71.8 - - + +
670D GLU* 3.6 3.6 - - + +
671D GLU* 3.1 32.4 + - + +
672D ARG* 3.0 26.4 + - - +
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Residues in contact with PRO 669 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667D VAL 4.8 0.4 - - - +
668D ALA* 1.4 84.7 - - + +
670D GLU* 1.3 67.6 + - + +
671D GLU 3.2 0.2 + - - -
672D ARG* 3.3 25.3 + - - +
673D HIS* 3.1 25.9 + - - +
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Residues in contact with GLU 670 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641C PRO* 6.0 0.2 - - - +
642C ASN* 3.3 22.4 + - - +
644C ALA* 3.8 25.6 - - + +
645C SER* 5.5 0.7 + - - -
648C GLU* 4.3 15.9 - - - +
668D ALA* 3.6 2.9 - - + -
669D PRO* 1.3 78.6 - - + +
671D GLU* 1.3 63.5 + - + +
673D HIS* 4.0 1.2 - - - +
674D LEU* 2.9 36.5 + - + +
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Residues in contact with GLU 671 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667D VAL* 3.7 17.8 - - + +
668D ALA* 3.1 37.6 + - + +
669D PRO 3.1 0.6 - - - -
670D GLU* 1.3 78.7 - - + +
672D ARG* 1.3 65.0 + - - +
674D LEU* 3.4 9.3 + - + +
675D SER* 3.1 27.7 + - - -
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Residues in contact with ARG 672 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667D VAL* 4.2 26.5 + - + +
668D ALA 3.0 13.0 + - - +
669D PRO* 3.7 31.4 + - - +
671D GLU* 1.3 74.8 - - - +
673D HIS* 1.3 65.4 + - - +
675D SER* 3.4 6.7 + - - -
676D LYS* 3.1 58.7 + - + +
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Residues in contact with HIS 673 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647C SER* 5.2 0.6 + - - -
648C GLU* 3.5 40.8 + - + +
651C GLN* 2.6 35.9 + - - -
669D PRO 3.1 14.0 + - - +
670D GLU 4.0 2.7 - - - +
672D ARG* 1.3 80.6 - - - +
674D LEU* 1.3 56.8 + - - +
676D LYS* 3.3 22.2 + - + +
677D MET* 2.8 51.0 + - + +
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Residues in contact with LEU 674 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614C VAL* 4.0 27.1 - - + -
618C VAL* 4.7 17.7 - - + +
642C ASN* 4.3 16.8 - - - +
644C ALA* 3.9 39.3 - - + +
647C SER* 4.8 1.8 - - - +
648C GLU* 5.4 0.2 + - - -
670D GLU* 2.9 24.8 + - + +
671D GLU* 3.5 9.6 - - + +
673D HIS* 1.3 78.8 + - - +
675D SER* 1.3 56.9 + - - +
677D MET* 3.1 6.4 + - + +
678D GLN* 3.0 39.8 + - - +
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Residues in contact with SER 675 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671D GLU 3.1 15.9 + - - -
672D ARG* 3.4 8.3 + - - -
674D LEU* 1.3 71.3 - - - +
676D LYS* 1.3 60.8 + - - +
678D GLN* 3.4 12.1 + - - +
679D GLN* 2.9 54.8 + - - +
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Residues in contact with LYS 676 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672D ARG* 3.1 63.7 + - - +
673D HIS* 3.3 22.7 - - + +
675D SER* 1.3 77.4 - - - +
677D MET* 1.3 65.4 + - + +
679D GLN* 4.8 4.5 - - - -
680D ASN* 3.1 32.3 + - - +
681D GLY 3.5 5.2 + - - +
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Residues in contact with MET 677 (chain D).
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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612C LEU* 3.3 28.9 - - + -
613C ALA* 3.5 6.6 - - - +
614C VAL* 3.3 26.8 + - + -
647C SER* 4.0 22.2 - - - +
651C GLN* 4.1 17.7 - - - +
673D HIS* 2.8 34.4 + - + +
674D LEU* 3.1 11.9 + - - +
676D LYS* 1.3 78.1 - - + +
678D GLN* 1.3 58.1 + - - +
681D GLY* 3.2 30.8 + - - +
682D TYR* 3.7 25.4 - - + -
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Residues in contact with GLN 678 (chain D).
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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559C VAL* 3.5 14.7 - - - +
563C ASN* 5.1 0.9 + - - -
614C VAL* 3.4 21.2 - - + +
615C GLY 2.8 29.4 + - - +
616C ARG* 3.0 43.2 + - - +
618C VAL* 3.4 29.3 - - - +
674D LEU* 3.0 21.8 + - - +
675D SER* 3.7 13.8 + - - +
676D LYS 3.3 0.2 - - - -
677D MET* 1.3 75.6 - - - +
679D GLN* 1.3 64.8 + - + +
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Residues in contact with GLN 679 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559C VAL* 3.8 15.7 - - - +
616C ARG* 3.9 15.4 + - - +
675D SER* 2.9 46.8 + - - +
676D LYS* 4.2 3.1 - - - +
678D GLN* 1.3 77.0 - - + +
680D ASN* 1.3 75.2 + - - +
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Residues in contact with ASN 680 (chain D).
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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559C VAL* 3.7 7.2 - - - +
611C PHE* 3.6 15.2 - - - -
676D LYS* 3.1 16.4 + - - +
679D GLN* 1.3 90.6 + - - +
681D GLY* 1.3 72.7 + - - +
683D GLU* 5.9 0.5 - - - +
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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