Contacts of the strand formed by residues 267 - 273 (chain I) in PDB entry 4DHJ
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 HIS 267 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82I ILE 2.9 22.7 + - - -
84I GLY* 3.6 19.0 - - - -
88I CYS* 3.8 6.7 - - + -
262I LEU 3.4 2.3 - - - +
263I TYR* 3.5 7.7 - - - -
264I ARG* 2.6 56.7 + - + +
265I PRO 4.4 3.4 - - - +
266I GLY* 1.3 75.5 - - - +
268I TYR* 1.3 80.3 + - - +
269I ASP* 2.7 40.4 + - - -
576J GLZ 3.1 19.4 + - - +
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Residues in contact with TYR 268 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82I ILE* 3.6 12.4 - - - +
88I CYS* 3.5 14.8 - - - +
89I PHE* 3.9 37.0 - + + -
92I ALA* 4.5 7.2 - - + -
218I ILE* 3.3 17.8 - - + +
231I ILE* 4.3 19.4 - - + +
261I LEU* 4.0 18.6 - - + -
262I LEU 3.3 10.3 - - - -
263I TYR* 3.2 33.6 - + + -
267I HIS* 1.3 92.4 + - - +
269I ASP* 1.3 65.4 + - - +
573J LEU* 2.6 38.9 + - - +
575J GLY* 3.7 15.9 - - - -
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Residues in contact with ASP 269 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79I ILE* 4.2 16.3 - - + +
80I ARG 3.6 9.2 - - - +
81I TYR* 3.3 14.4 - - - -
82I ILE* 2.8 25.6 + - - +
92I ALA* 4.8 0.4 - - - -
261I LEU* 3.3 10.8 - - - +
262I LEU* 2.9 35.4 + - + +
264I ARG* 2.8 33.3 + - - -
267I HIS* 2.7 27.8 + - - -
268I TYR* 1.3 71.7 - - - +
270I VAL* 1.3 64.6 + - - +
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Residues in contact with VAL 270 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79I ILE* 3.7 0.5 - - - +
80I ARG* 2.8 37.9 + - + +
82I ILE* 4.2 10.8 - - + -
92I ALA* 3.7 41.3 - - + +
95I VAL* 4.6 8.1 - - + -
96I GLY* 5.4 2.2 - - - -
99I GLU* 4.5 3.1 - - - +
259I ILE* 4.9 7.6 - - + -
260I THR 3.7 10.8 - - - +
261I LEU* 3.9 4.5 - - + -
269I ASP* 1.3 72.2 - - - +
271I ILE* 1.3 73.7 + - - +
272I TYR* 3.3 33.6 - - + +
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Residues in contact with ILE 271 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50I PHE* 3.7 24.9 - - + -
72I LEU* 5.7 0.2 - - + -
76I TYR* 3.8 24.2 - - + -
78I GLU 3.4 7.4 - - - +
79I ILE* 3.9 13.2 - - + -
232I GLU* 3.9 18.2 - - + -
260I THR* 3.0 54.0 + - + +
261I LEU 4.2 0.7 - - - +
262I LEU* 3.8 32.5 - - + +
270I VAL* 1.3 83.8 - - - +
272I TYR* 1.3 70.7 + - - +
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Residues in contact with TYR 272 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47I LEU* 3.4 29.2 - - + -
76I TYR* 3.5 5.3 - - - -
77I GLY 2.8 30.7 + - - -
78I GLU* 3.1 32.9 + - + +
80I ARG* 2.9 23.5 + - + -
95I VAL* 4.6 0.2 - - - +
99I GLU* 2.6 43.0 + - - -
260I THR* 5.6 0.2 - - - -
270I VAL* 3.3 28.1 - - + +
271I ILE* 1.3 81.7 - - - +
273I LYS* 1.3 60.4 + - - +
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Residues in contact with LYS 273 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75I VAL* 3.4 33.6 - - + +
76I TYR* 3.6 22.1 - - + +
77I GLY* 5.1 0.3 - - - -
78I GLU* 5.7 0.5 - - - +
257I PRO* 6.3 4.0 - - + -
260I THR* 5.4 4.7 - - - +
272I TYR* 1.3 78.9 - - - +
274I LYS* 1.3 71.1 + - - +
275I ASP* 3.6 1.6 + - - -
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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