Contacts of the strand formed by residues 655 - 662 (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 SER 655 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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506D ILE* 5.6 0.4 - - - -
653D TYR 3.4 1.8 - - - -
654D VAL* 1.3 88.6 - - - +
656D GLY* 1.3 56.1 + - - +
671D ASP* 6.0 0.4 - - - -
673D PHE* 3.1 24.1 - - - -
706D LEU* 3.6 2.1 - - - +
707D GLU* 2.7 54.9 + - - +
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Residues in contact with GLY 656 (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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655D SER* 1.3 77.7 - - - +
657D ARG* 1.3 66.2 + - - +
671D ASP* 3.4 9.1 + - - +
672D LEU* 3.1 23.4 + - - +
673D PHE* 3.3 8.8 + - - -
705D TYR* 2.8 16.2 - - - -
706D LEU* 4.2 1.1 - - - -
707D GLU* 3.7 10.4 + - - -
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Residues in contact with ARG 657 (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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406C VAL* 3.6 37.1 + - - +
407C HIS* 3.9 4.8 + - - +
656D GLY* 1.3 76.7 - - - +
658D ILE* 1.3 70.4 + - - +
659D GLU* 4.0 21.8 + - - +
669D GLN* 4.7 13.1 - - + +
670D ILE 4.4 0.9 - - - +
671D ASP* 4.2 14.4 - - - +
672D LEU* 3.6 18.1 - - - +
704D ILE* 3.6 3.5 - - - -
705D TYR* 2.9 78.7 + - + +
707D GLU* 5.1 6.1 + - - -
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Residues in contact with ILE 658 (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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632D ILE* 5.9 0.2 - - + -
633D ASP* 3.8 23.3 - - - +
636D ILE* 3.4 44.6 - - + -
637D ARG* 4.7 0.2 - - + -
657D ARG* 1.3 79.9 - - - +
659D GLU* 1.3 66.0 + - - +
660D ILE* 4.0 26.5 - - + -
668D GLU 3.3 1.0 - - - +
669D GLN* 3.2 6.4 - - - +
670D ILE* 2.9 42.8 + - + +
672D LEU* 3.7 28.5 - - + -
702D PHE* 5.2 0.7 - - + -
703D ASP 3.6 5.8 - - - +
704D ILE* 4.9 4.5 - - + -
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Residues in contact with GLU 659 (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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407C HIS* 3.0 33.8 + - - -
657D ARG* 4.0 20.7 + - - +
658D ILE* 1.3 77.4 - - - +
660D ILE* 1.3 63.1 + - - +
661D GLY 3.2 1.4 + - - -
667D HIS* 3.5 27.8 - - + +
668D GLU 3.4 3.4 - - - -
669D GLN* 4.1 19.2 + - - +
702D PHE* 3.1 8.8 - - - +
703D ASP* 2.8 49.3 + - + +
705D TYR* 4.0 20.5 + - + -
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Residues in contact with ILE 660 (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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629D PHE* 3.6 40.4 - - + -
632D ILE* 3.7 30.1 - - + -
636D ILE* 4.6 0.2 - - + -
658D ILE* 4.0 17.0 - - + -
659D GLU* 1.3 72.3 - - - +
661D GLY* 1.3 62.6 + - - +
662D THR* 3.5 10.8 + - - +
666D LYS 3.7 1.0 - - - +
667D HIS* 4.3 0.4 - - - -
668D GLU* 2.9 36.6 + - + +
670D ILE* 4.2 8.5 - - + -
694D ILE* 4.2 10.5 - - + -
699D PHE* 3.8 29.2 - - + -
701D HIS 4.3 0.7 - - - -
702D PHE* 4.3 7.4 - - + -
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Residues in contact with GLY 661 (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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659D GLU 3.2 6.9 + - - -
660D ILE* 1.3 72.1 - - - +
662D THR* 1.3 61.8 + - - -
666D LYS 3.4 8.7 - - - -
667D HIS* 4.2 6.7 - - - -
699D PHE* 3.9 6.8 - - - -
700D SER* 2.9 18.7 + - - -
701D HIS* 2.7 45.2 + - - +
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Residues in contact with THR 662 (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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280B ARG* 4.5 2.9 - - - +
660D ILE* 3.5 11.8 + - - +
661D GLY* 1.3 75.6 - - - -
663D LYS* 1.3 60.7 + - - +
664D ASP* 2.9 33.2 + - + +
665D GLY* 3.1 18.0 + - - -
666D LYS* 3.0 11.9 + - - +
668D GLU* 4.7 10.0 + - - +
694D ILE* 5.5 5.3 - - + +
698D ASN* 2.9 36.6 - - + +
699D PHE* 4.6 0.9 - - - +
700D SER* 3.4 10.5 + - - -
701D HIS* 5.4 1.4 + - - -
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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