Contacts of the strand formed by residues 267 - 276 (chain I) in PDB entry 3PB1
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 THR 267 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208I PHE 3.4 1.0 - - - +
209I ASN* 3.4 5.2 - - - -
210I TYR 2.9 29.7 + - - +
265I ASN 3.8 4.6 + - - -
266I MET* 1.3 75.0 + - - +
268I ARG* 1.3 74.1 + - - +
269I LEU* 3.5 24.1 + - + +
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Residues in contact with ARG 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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176I LYS* 5.4 6.7 - - - +
206I ASN* 5.4 0.6 - - - +
207I LYS* 3.2 43.0 + - + +
208I PHE 3.5 6.7 - - - +
209I ASN* 3.2 24.7 - - - +
267I THR* 1.3 74.5 - - - +
269I LEU* 1.3 67.6 + - - +
270I PRO* 4.7 1.0 - - - +
341I VAL* 2.9 47.4 - - - +
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Residues in contact with LEU 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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60E ASP* 5.5 8.1 - - + -
207I LYS* 3.3 3.8 - - - -
208I PHE 2.9 32.5 + - - +
210I TYR* 3.8 31.6 - - + +
267I THR* 3.6 27.6 - - + +
268I ARG* 1.3 82.7 - - - +
270I PRO* 1.3 76.2 - - + +
271I ARG* 3.4 33.1 + - + +
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Residues in contact with PRO 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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60E ASP* 4.7 13.5 - - + -
206I ASN 3.5 6.7 - - - +
207I LYS* 4.2 15.4 - - + -
268I ARG 4.7 1.1 - - - +
269I LEU* 1.3 89.6 - - + +
271I ARG* 1.3 87.2 + - - +
343I VAL* 3.8 28.5 - - + -
345I ALA* 6.2 0.7 - - + -
347I MET* 6.2 4.5 - - - -
349I PRO* 5.4 5.5 - - + +
350I GLU* 4.6 4.2 + - - +
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Residues in contact with ARG 271 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E ASP* 4.6 10.3 - - - +
205I THR* 3.3 2.6 - - - -
206I ASN 2.8 31.7 + - - +
208I PHE* 3.6 20.9 - - + -
210I TYR* 4.8 12.7 - - + -
224I LEU* 5.2 2.7 - - + -
269I LEU* 3.9 43.3 - - + +
270I PRO* 1.3 105.9 + - - +
272I LEU* 1.3 61.5 + - - +
273I LEU* 5.7 0.2 - - - -
343I VAL* 4.9 1.2 - - - +
349I PRO* 4.5 6.7 - - - +
350I GLU* 3.3 56.1 + - - +
352I ILE* 3.6 35.6 - - + +
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Residues in contact with LEU 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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143E LYS* 3.3 30.5 - - - +
148E ASP 5.2 0.4 - - - +
149E TYR* 4.4 9.4 - - + -
151E TYR* 5.4 0.2 - - - +
203I ALA* 4.2 10.8 - - + -
204I GLN 3.5 9.6 - - - +
205I THR* 3.5 19.5 - - + -
271I ARG* 1.3 73.2 - - - +
273I LEU* 1.3 76.4 + - - +
274I VAL* 3.8 16.1 + - + -
349I PRO* 3.9 15.3 - - + +
350I GLU 2.9 12.1 + - - +
351I GLU* 3.2 28.2 - - + +
352I ILE 2.8 27.9 + - - +
353I ILE* 4.9 0.2 - - - +
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Residues in contact with LEU 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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179I PHE* 4.5 9.6 - - + -
202I MET 3.7 0.7 - - - +
203I ALA* 3.2 5.5 - - - -
204I GLN 2.9 31.8 + - - -
208I PHE* 3.8 23.1 - - + -
224I LEU* 3.5 29.2 - - + -
226I LEU* 3.7 39.5 - - + -
237I ILE* 5.6 1.1 - - + -
271I ARG* 3.9 2.0 - - + -
272I LEU* 1.3 75.4 - - - +
274I VAL* 1.3 67.5 + - - +
275I LEU* 4.1 13.6 + - + -
352I ILE* 3.4 17.0 - - + +
354I ILE* 3.9 20.4 - - + -
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Residues in contact with VAL 274 (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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149E TYR* 4.0 16.6 - - + -
185I HIS* 4.3 4.3 - - + -
187I ARG* 3.8 17.9 - - - +
201I MET* 3.8 33.7 - - + -
202I MET 3.3 4.7 - - - +
203I ALA* 4.2 6.5 - - + -
272I LEU* 3.8 15.9 - - + -
273I LEU* 1.3 75.0 - - - +
275I LEU* 1.3 59.6 + - - +
352I ILE 3.0 7.4 + - - +
353I ILE* 3.6 31.9 - - + -
354I ILE* 2.9 32.9 + - - +
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Residues in contact with LEU 275 (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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175I TRP* 5.2 0.9 - - + -
179I PHE* 4.4 8.1 - - + -
201I MET* 4.1 2.0 - - - -
202I MET* 2.7 64.5 + - + +
226I LEU* 3.9 25.8 - - + -
235I MET* 5.6 0.9 - - - -
237I ILE* 3.8 26.0 - - + -
273I LEU* 4.0 14.1 - - + -
274I VAL* 1.3 73.7 - - - +
276I PRO* 1.3 80.9 - - + +
278I PHE* 5.1 2.5 - - + -
328I VAL* 4.6 10.5 - - + -
354I ILE* 4.1 19.3 - - + -
358I PHE* 4.3 10.8 - - + -
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Residues in contact with PRO 276 (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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189I PHE* 4.2 5.2 - - + -
199I VAL* 4.2 2.9 - - + -
200I PRO 3.5 12.8 - - - +
201I MET* 3.9 13.6 - - + -
202I MET* 4.1 2.9 - - - +
275I LEU* 1.3 101.8 - - + +
277I LYS* 1.3 65.7 + - - +
278I PHE* 3.4 14.4 - - - -
354I ILE 3.1 25.8 - - - +
358I PHE* 4.0 14.6 - - + -
379I PRO* 3.6 33.0 - - + +
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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