Contacts of the strand formed by residues 267 - 271 (chain C) in PDB entry 3Q41
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 ILE 267 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C MET* 3.7 17.9 - - + -
160C TRP* 6.2 0.7 - - + -
246C VAL* 5.5 2.2 - - + -
247C TRP 2.8 17.9 + - - +
248C LEU* 3.6 15.2 - - + -
249C VAL* 2.8 37.3 + - - +
265C GLY 4.1 6.3 - - - +
266C ILE* 1.3 71.9 - - - +
268C GLY* 1.3 59.5 + - - +
269C LEU* 5.7 1.6 - - + -
353C ILE* 3.7 24.0 - - + -
354C MET 3.3 6.7 - - - +
355C ASN* 3.1 37.5 - - + +
364C VAL* 4.9 0.4 - - + -
379C ILE* 3.7 22.4 - - + -
381C TRP* 4.3 15.9 - - + -
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Residues in contact with GLY 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C VAL* 3.8 6.7 - - - -
250C GLY 3.7 12.8 - - - -
254C ILE* 3.8 19.3 - - - +
266C ILE* 4.0 1.6 + - - +
267C ILE* 1.3 76.9 - - - +
269C LEU* 1.3 66.4 + - - +
353C ILE* 3.9 0.2 - - - -
354C MET 2.7 35.6 + - - -
361C LEU* 5.5 0.8 - - - +
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Residues in contact with LEU 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C GLN* 3.7 36.6 - - + +
150C VAL* 3.7 45.3 - - + -
151C TRP* 3.9 17.3 - - + +
154C MET* 6.0 1.6 - - - -
248C LEU* 6.1 2.2 - - + -
249C VAL 4.0 6.3 - - - +
250C GLY* 3.4 8.1 + - - -
251C GLU* 3.1 18.8 - - - +
254C ILE* 3.4 10.3 - - - +
267C ILE* 5.7 2.0 - - + -
268C GLY* 1.3 82.1 - - - +
270C GLN* 1.3 69.8 + - - +
351C TYR* 4.8 9.2 - - + -
352C SER 3.6 7.0 - - - +
353C ILE* 3.8 20.9 - - + -
354C MET* 4.7 0.2 - - - -
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Residues in contact with GLN 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C GLU* 3.3 25.2 - - + +
254C ILE* 4.4 8.1 - - - +
269C LEU* 1.3 81.3 - - - +
271C LEU* 1.3 66.5 + - - +
272C ILE* 3.3 1.7 + - - +
351C TYR* 4.5 1.6 - - - -
352C SER* 3.1 37.5 + - - +
354C MET* 3.7 41.0 - - + +
361C LEU* 4.6 5.5 - - - +
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Residues in contact with LEU 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C ARG* 3.7 33.4 - - - +
141C VAL* 3.6 21.5 - - + -
142C PRO* 3.6 40.8 - - + -
251C GLU* 3.0 10.5 + - - +
270C GLN* 1.3 70.1 - - - +
272C ILE* 1.3 65.8 + - - +
273C ASN 3.5 0.2 + - - -
274C GLY* 3.0 31.2 + - - -
275C LYS* 5.6 0.9 - - - +
280C HIS* 5.4 1.6 - - + +
349C ALA* 4.2 15.0 - - + -
350C ASN 3.7 18.2 - - - +
351C TYR* 4.1 15.0 - - + -
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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