Contacts of the helix formed by residues 643 - 652 (chain D) in PDB entry 5UHA
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 643 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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642D PRO* 1.3 92.1 - - + +
644D VAL* 1.3 55.8 + - - +
645D GLU* 3.2 5.2 - - + +
646D ILE* 3.1 30.1 + - + +
647D GLU* 2.7 33.3 + - - +
662D TRP* 3.7 18.6 - - + -
682D PRO* 4.7 3.4 - - + -
683D PHE* 4.2 26.7 - - + +
685D ASN* 6.3 2.2 - - + +
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Residues in contact with VAL 644 (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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641D ARG* 6.1 3.8 - - - +
642D PRO 4.6 0.4 - - - +
643D PRO* 1.3 73.0 - - - +
645D GLU* 1.3 62.3 + - - +
646D ILE 3.4 0.3 + - - -
647D GLU* 4.1 11.9 - - - +
648D ALA* 3.4 22.7 + - - +
653D HIS* 6.5 0.9 - - + -
682D PRO* 4.1 25.5 - - + +
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Residues in contact with GLU 645 (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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643D PRO* 3.2 4.7 - - + +
644D VAL* 1.3 79.8 - - - +
646D ILE* 1.3 80.8 + - + +
648D ALA* 4.0 4.5 + - - +
649D GLU* 3.8 27.0 + - - +
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Residues in contact with ILE 646 (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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642D PRO* 4.5 1.6 - - + -
643D PRO* 3.1 36.6 + - + +
645D GLU* 1.3 95.6 - - - +
647D GLU* 1.3 63.9 + - - +
648D ALA 3.2 2.0 - - - -
649D GLU* 3.3 10.6 + - - +
650D LEU* 3.0 47.7 + - + +
662D TRP* 4.6 16.8 - - + -
663D MET 5.5 1.6 - - - +
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Residues in contact with GLU 647 (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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641D ARG* 3.6 32.2 + - - -
642D PRO* 3.8 22.8 - - + +
643D PRO 2.7 21.1 + - - +
644D VAL* 4.1 11.9 - - - +
646D ILE* 1.3 72.5 - - - +
648D ALA* 1.3 58.0 + - - +
651D PHE* 2.9 46.7 + - + +
652D GLY 3.6 0.3 + - - -
653D HIS* 3.9 23.3 + - - -
655D GLY* 4.1 1.9 + - - -
656D TRP* 3.1 39.3 + - + +
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Residues in contact with ALA 648 (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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644D VAL 3.4 14.9 + - - +
645D GLU* 4.2 6.5 - - - +
646D ILE 3.2 0.4 - - - -
647D GLU* 1.3 80.9 - - - +
649D GLU* 1.3 57.0 + - - +
652D GLY* 2.9 25.1 + - - -
653D HIS* 3.9 19.0 - - + +
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Residues in contact with GLU 649 (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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645D GLU* 3.8 22.8 + - - +
646D ILE* 3.3 15.0 + - - +
648D ALA* 1.3 79.1 - - - +
650D LEU* 1.3 76.6 + - + +
652D GLY 4.6 0.7 + - - -
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Residues in contact with LEU 650 (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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642D PRO* 5.8 0.9 - - + -
646D ILE* 3.0 34.5 + - + +
649D GLU* 1.3 101.3 - - + +
651D PHE* 1.3 82.9 + - + +
662D TRP* 4.0 28.5 - - + -
663D MET 5.0 5.4 - - - +
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Residues in contact with PHE 651 (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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642D PRO* 4.7 6.7 - - + -
647D GLU* 2.9 30.4 + - + +
649D GLU 3.5 0.2 - - - -
650D LEU* 1.3 104.4 - - + +
652D GLY* 1.3 65.2 + - - +
653D HIS 4.1 0.4 - - - +
654D SER* 3.1 37.3 + - - +
655D GLY 5.0 2.7 - - - +
656D TRP* 3.8 22.7 - + - +
660D ASP* 3.1 44.9 - - + -
661D ALA 4.0 17.3 - - - -
662D TRP* 4.8 4.0 - - + -
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Residues in contact with GLY 652 (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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647D GLU 3.6 0.2 + - - -
648D ALA* 2.9 21.9 + - - -
649D GLU 4.6 0.4 - - - -
651D PHE* 1.3 75.1 - - - +
653D HIS* 1.3 72.3 + - - +
654D SER* 3.3 1.0 + - - -
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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