Contacts of the strand formed by residues 699 - 707 (chain D) in PDB entry 1HQR
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 PHE 699 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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602D LEU* 3.9 30.1 - - + -
603D LEU 4.6 1.3 - - - -
632D ILE* 3.4 29.2 - - + -
660D ILE* 3.8 17.9 - - + -
661D GLY 3.9 4.0 - - - -
663D LYS* 3.7 10.3 - - - -
694D ILE* 3.4 29.8 - - + +
695D ASN 3.5 1.6 + - - -
696D MET* 3.0 39.2 + - + +
698D ASN* 1.3 77.0 - - - +
700D SER* 1.3 66.8 + - - +
701D HIS* 3.5 30.3 - - - -
702D PHE* 4.0 19.3 - + + -
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Residues in contact with SER 700 (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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276B ASP* 3.0 36.3 + - - +
280B ARG* 4.1 7.3 - - - +
603D LEU* 4.2 8.7 + - - +
661D GLY 2.9 9.6 + - - -
662D THR 3.4 27.8 - - - -
663D LYS* 3.6 15.4 - - - +
698D ASN 3.2 2.8 + - - -
699D PHE* 1.3 77.2 - - - +
701D HIS* 1.3 77.0 + - - +
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Residues in contact with HIS 701 (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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276B ASP 3.5 8.6 + - - -
277B THR* 3.9 19.5 - - + +
280B ARG* 4.9 1.3 - - + -
281B HIS* 3.1 24.3 + - + +
603D LEU* 3.5 15.7 - - + +
605D ASN* 4.0 9.2 - - - -
661D GLY* 2.7 45.5 + - - +
662D THR 5.4 1.6 - - - -
667D HIS* 4.1 3.8 - + - -
699D PHE* 3.5 12.6 - - - -
700D SER* 1.3 102.5 + - - +
702D PHE* 1.3 60.8 + - - +
703D ASP* 3.0 17.7 + - - -
709D ZN 2.1 34.3 - - - -
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Residues in contact with PHE 702 (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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602D LEU* 3.8 24.7 - - + -
603D LEU 3.1 26.6 + - - -
604D GLY* 3.1 23.6 - - - -
605D ASN 3.0 23.4 + - - -
616D LEU* 4.4 20.4 - - + -
620D ILE* 4.6 13.7 - - + -
636D ILE* 4.0 21.8 - - + -
639D TYR* 6.5 0.2 - + - -
658D ILE* 5.2 0.9 - - + -
659D GLU 3.1 13.5 - - - +
660D ILE* 4.3 10.3 - - + -
699D PHE* 4.0 21.3 - + + -
701D HIS* 1.3 79.9 - - - +
703D ASP* 1.3 67.2 + - - +
704D ILE* 4.0 31.9 - - + -
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Residues in contact with ASP 703 (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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281B HIS* 2.8 22.6 - - + -
605D ASN* 2.9 26.2 + - - +
607D PHE* 4.4 3.6 - - + -
657D ARG 4.0 0.3 - - - +
658D ILE* 3.6 4.9 - - - +
659D GLU* 2.8 36.0 + - + +
667D HIS* 3.0 13.0 - - - -
701D HIS* 3.0 5.6 + - - -
702D PHE* 1.3 73.0 - - - +
704D ILE* 1.3 65.1 + - - +
705D TYR* 3.8 21.3 - - + -
709D ZN 1.9 33.2 - - - -
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Residues in contact with ILE 704 (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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605D ASN 2.8 11.7 + - - +
606D LEU* 3.1 24.7 - - + -
607D PHE* 2.7 36.1 + - - +
616D LEU* 4.1 16.4 - - + -
636D ILE* 3.8 18.2 - - + -
639D TYR* 5.5 0.7 - - + -
640D LEU* 3.6 42.6 - - + -
657D ARG 3.6 9.6 - - - +
658D ILE* 4.9 3.4 - - + -
672D LEU* 4.7 0.7 - - + -
702D PHE* 4.0 17.5 - - + -
703D ASP* 1.3 79.8 - - - +
705D TYR* 1.3 62.5 + - - +
706D LEU* 4.2 11.4 - - + -
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Residues in contact with TYR 705 (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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281B HIS* 4.1 12.0 - - - -
406C VAL 3.9 5.8 - - - -
407C HIS* 4.0 6.8 + - - -
408C PHE* 3.4 54.2 + + + +
607D PHE* 3.1 30.5 - + + -
656D GLY* 2.8 25.6 - - - -
657D ARG* 2.9 64.3 + - + +
659D GLU* 4.0 11.2 + - + -
703D ASP* 3.8 20.6 - - + -
704D ILE* 1.3 78.0 - - - +
706D LEU* 1.3 66.6 + - - +
707D GLU* 4.2 11.9 - - - +
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Residues in contact with LEU 706 (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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606D LEU* 4.4 11.7 - - + -
607D PHE 2.9 7.1 + - - -
608D ILE* 3.2 25.2 - - + +
609D SER 2.6 30.8 + - - -
640D LEU* 4.7 5.8 - - + -
644D TYR* 4.8 4.3 - - + -
646D ILE* 4.0 25.4 - - + -
653D TYR* 3.6 30.7 - - + -
655D SER 3.6 1.3 - - - +
672D LEU* 4.2 14.6 - - + -
673D PHE* 4.1 27.4 - - + -
704D ILE* 4.2 9.9 - - + -
705D TYR* 1.3 82.1 - - - +
707D GLU* 1.3 59.0 + - - +
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Residues in contact with GLU 707 (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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408C PHE* 5.8 2.6 - - - -
607D PHE 5.4 0.2 - - - +
609D SER* 3.6 21.3 + - - -
653D TYR* 2.9 21.9 - - - -
654D VAL* 2.9 11.1 + - + -
655D SER* 2.7 46.4 + - - +
656D GLY* 3.7 7.6 + - - -
657D ARG* 5.1 5.0 + - - -
705D TYR* 4.2 13.3 - - - +
706D LEU* 1.3 81.3 + - - +
708D LYS* 1.3 71.0 + - - +
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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