Contacts of the strand formed by residues 80 - 85 (chain A) in PDB entry 2P28
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 LYS 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A THR* 4.3 0.7 - - - -
66A GLN* 3.5 20.4 + - + -
67A GLU* 3.3 55.4 + - + +
78A PRO* 3.7 5.5 - - - +
79A GLN* 1.3 101.9 + - + +
81A VAL* 1.3 70.4 + - - +
416B THR* 3.4 23.4 + - + +
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Residues in contact with VAL 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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63A ALA* 4.7 0.4 - - + -
64A GLU 3.6 16.6 - - - +
65A THR* 4.8 4.0 - - - +
66A GLN* 4.5 2.9 - - - +
78A PRO* 3.5 24.0 - - + -
80A LYS* 1.3 81.3 - - - +
82A THR* 1.3 66.9 + - - +
83A LEU* 3.9 24.0 - - + -
93A PHE* 3.8 36.6 - - + -
415B VAL* 3.8 10.3 - - + -
416B THR 3.0 7.5 + - - +
417B VAL* 3.5 5.6 - - + -
418B GLN* 2.8 27.2 + - - +
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Residues in contact with THR 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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62A LEU 3.9 0.7 - - - +
63A ALA 3.7 0.5 - - - -
64A GLU* 2.8 45.4 + - - +
66A GLN* 3.1 31.8 + - - +
81A VAL* 1.3 73.9 + - - +
83A LEU* 1.3 66.5 + - - +
84A TYR* 3.6 30.6 + - + +
418B GLN* 2.9 37.6 + - + +
420B LEU* 4.2 8.7 - - + -
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Residues in contact with LEU 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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62A LEU 3.5 2.0 - - - +
63A ALA* 3.5 32.8 - - + -
81A VAL* 3.9 4.9 - - + -
82A THR* 1.3 76.8 - - - +
84A TYR* 1.3 58.8 + - - +
85A LEU* 4.0 14.4 + - + +
91A ALA* 4.2 11.4 - - + +
93A PHE* 3.8 18.6 - - + -
393B VAL* 3.4 43.1 - - + -
417B VAL* 3.7 22.9 - - + -
418B GLN 2.8 12.4 + - - +
419B VAL* 3.5 4.4 - - + -
420B LEU* 2.8 34.5 + - - +
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Residues in contact with TYR 84 (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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61A SER* 3.0 24.3 - - - -
62A LEU* 3.0 43.8 + - + +
64A GLU* 3.8 25.6 + - - -
66A GLN* 5.5 0.3 + - - -
82A THR* 3.6 20.5 - - + +
83A LEU* 1.3 73.5 - - - +
85A LEU* 1.3 62.2 + - - +
86A ARG 3.9 0.4 - - - -
420B LEU* 3.3 42.1 - - + +
421B PRO 4.0 11.0 - - - -
422B GLN* 4.0 22.4 - - + +
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Residues in contact with LEU 85 (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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61A SER* 3.6 2.9 - - - +
83A LEU* 4.0 13.0 - - + -
84A TYR* 1.3 72.5 - - - +
86A ARG* 1.3 63.2 + - - +
87A PRO* 3.6 6.2 - - - +
89A GLN 4.8 0.9 - - - +
91A ALA* 3.6 22.7 - - + +
356B LEU* 3.7 22.9 - - + -
393B VAL* 3.5 37.0 - - + +
394B THR* 5.0 0.4 - - - -
395B ALA* 4.0 21.1 - - + +
397B GLU 5.2 0.9 - - - +
398B CYS* 5.7 0.2 - - - -
399B ILE* 4.6 3.5 - - + +
419B VAL* 3.4 32.5 - - + -
420B LEU 2.9 10.8 + - - +
421B PRO* 4.0 3.5 - - - +
422B GLN* 3.1 17.8 + - - +
423B CYS* 4.8 0.7 - - - -
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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