Contacts of the strand formed by residues 540 - 544 (chain D) in PDB entry 6DV9
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 GLN 540 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1040C LYS* 3.6 49.6 - - + +
427D ARG* 3.5 48.6 + - - +
428D SER 3.2 18.2 - - - +
429D VAL* 4.2 7.4 - - + +
430D ILE* 4.5 0.7 - - - +
500D ARG* 4.2 13.7 - - - +
501D ALA 5.2 0.3 + - - -
538D GLY 3.8 6.0 + - - +
539D ASP* 1.3 79.7 - - - +
541D MET* 1.3 67.0 + - - +
17G G 4.9 13.6 + - - +
18G A 6.1 0.7 - - - +
6I G 4.9 12.1 + - - +
7I A 5.9 0.6 - - - -
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Residues in contact with MET 541 (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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427D ARG* 3.2 28.1 - - - +
428D SER 3.0 10.9 + - - +
430D ILE* 3.5 35.1 - - + +
498D LEU* 4.3 15.7 - - + -
499D ASN 3.2 20.2 - - - +
500D ARG* 3.6 16.8 - - + -
522D ILE* 3.9 10.3 - - + +
524D LEU* 3.7 31.6 - - + -
532D PHE* 3.5 40.2 - - + -
534D ALA* 4.0 1.8 - - + -
540D GLN* 1.3 74.5 - - - +
542D ALA* 1.3 63.8 + - - +
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Residues in contact with ALA 542 (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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1066C GLN* 4.2 19.1 - - + +
426D GLY 3.2 11.2 - - - +
427D ARG* 4.2 9.1 - - + +
497D LEU 3.5 0.7 - - - +
498D LEU* 3.4 7.3 - - - +
499D ASN* 2.9 42.0 + - + +
541D MET* 1.3 74.2 - - - +
543D VAL* 1.3 62.5 + - - +
544D HIS* 3.9 20.6 - - - +
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Residues in contact with VAL 543 (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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425D SER* 3.1 10.2 - - - -
426D GLY 2.7 36.8 + - - +
443D LEU* 4.5 7.6 - - + -
447D MET* 3.6 18.8 - - + -
451D LEU* 4.1 20.8 - - + +
496D VAL* 4.0 22.4 - - + -
497D LEU 3.2 8.7 - - - +
498D LEU* 3.7 14.6 - - + -
522D ILE* 3.6 28.9 - - + -
542D ALA* 1.3 77.0 - - - +
544D HIS* 1.3 67.1 + - - +
545D LEU* 5.9 0.4 - - + -
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Residues in contact with HIS 544 (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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1066C GLN* 4.0 12.8 - - + -
1067C ARG 5.1 0.8 + - - -
1068C PHE* 3.9 34.9 - + + -
1088C LEU* 4.3 6.4 - - + +
1092C LYS* 4.5 9.2 - - - +
422D VAL* 3.5 31.6 - - + +
424D TYR 3.8 3.3 + - - -
425D SER* 3.6 12.7 - - - -
451D LEU* 6.1 0.2 - - - -
496D VAL* 3.8 2.1 - - - +
497D LEU* 2.9 53.4 + - + +
499D ASN* 4.8 13.4 + - + -
509D ILE* 6.0 1.1 - - + -
542D ALA* 3.9 21.4 - - + +
543D VAL* 1.3 79.9 - - - +
545D LEU* 1.3 60.1 + - - +
546D PRO* 3.4 5.1 - - - +
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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