Contacts of the strand formed by residues 78 - 83 (chain A) in PDB entry 1D7W
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 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A LEU* 3.5 18.3 - - + +
77A THR* 1.3 97.1 - - + +
79A ASP* 1.3 63.3 + - - +
80A GLN* 3.3 15.4 + - + +
340C GLN* 4.8 4.7 - - - +
388C PRO* 4.1 20.4 - - + -
389C ALA 3.9 5.6 - - - +
391C LEU* 4.5 1.0 - - - +
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Residues in contact with ASP 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A THR 3.5 1.6 + - - -
78A PRO* 1.3 68.7 - - - +
80A GLN* 1.3 60.2 + - - +
81A GLU 2.9 20.4 + - - -
82A ARG* 3.1 30.1 - - + +
338C LEU* 5.5 1.7 - - - +
388C PRO* 3.2 4.4 - - - +
389C ALA* 2.9 23.8 + - + +
390C LYS 4.4 1.1 - - - +
391C LEU* 3.6 26.0 - - + +
490C ARG* 2.7 41.8 + - - -
555C ASN* 2.9 21.0 + - - -
1610C SO4 4.4 0.5 + - - -
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Residues in contact with GLN 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A PRO* 3.3 14.1 + - + +
79A ASP* 1.3 74.5 + - - +
81A GLU* 1.4 73.8 + - + +
82A ARG 3.6 0.2 - - - -
388C PRO* 5.3 0.9 - - - -
553C MET 4.6 0.7 - - - +
555C ASN* 3.3 20.1 + - - +
559C ARG* 4.5 6.4 + - - -
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Residues in contact with GLU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ASP* 2.9 3.6 + - - -
80A GLN* 1.4 92.5 - - + +
82A ARG* 1.3 82.2 + - - +
490C ARG* 3.8 4.7 - - - +
553C MET* 3.2 47.9 - - + +
559C ARG* 5.2 5.7 + - - -
1610C SO4 3.1 34.0 + - - +
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Residues in contact with ARG 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ASP* 3.1 33.4 + - + +
80A GLN 3.6 0.6 - - - -
81A GLU* 1.3 101.5 + - - +
83A SER* 1.3 59.4 - - - +
86A PHE* 3.7 33.2 - - + -
299C LEU* 2.7 55.6 + - - +
388C PRO* 3.0 9.5 - - - +
389C ALA* 2.9 24.0 + - + -
488C LYS* 2.9 26.5 + - - +
490C ARG* 3.6 27.8 - - - +
552C PHE 3.2 15.3 - - - +
553C MET* 3.8 9.9 + - - +
555C ASN* 3.2 8.1 + - - -
1610C SO4 4.6 2.4 + - - -
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Residues in contact with SER 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ARG* 1.3 74.6 - - - +
84A LEU* 1.3 59.5 + - - +
85A MET* 3.0 14.9 - - - +
86A PHE* 3.0 26.7 + - - +
384C LEU 3.7 12.8 - - - -
385C MET* 4.0 5.4 - - - -
387C THR 3.3 7.9 - - - -
389C ALA* 3.5 6.9 - - - +
551C ILE 2.9 18.6 + - - -
552C PHE* 3.0 9.3 + - - -
553C MET 3.9 1.2 + - - -
554C SER 3.2 22.9 - - - -
555C ASN* 3.8 3.1 - - - -
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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