Contacts of the strand formed by residues 305 - 310 (chain C) in PDB entry 4K81
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 GLY 305 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C TRP* 6.1 0.2 - - - -
291C SER* 2.7 34.1 + - - -
302C THR 5.3 0.2 - - - -
303C ASN 2.7 15.1 + - - -
304C TYR* 1.3 73.2 - - - +
306C PHE* 1.3 60.8 + - - +
322C LEU 3.4 13.5 - - - -
323C CYS* 4.1 8.4 - - - -
330C ARG* 3.2 12.3 + - - -
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Residues in contact with PHE 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C LEU* 4.0 20.9 - - + -
288C ILE* 5.0 1.3 - - + -
289C TYR 3.2 16.4 - - - +
290C VAL* 4.2 2.5 - - - +
291C SER* 4.5 1.3 - - - +
304C TYR 4.0 2.5 - - - -
305C GLY* 1.3 76.8 - - - +
307C CYS* 1.3 65.2 + - - +
308C PHE* 4.3 10.5 - + - -
321C MET* 4.7 0.2 - - - +
322C LEU* 2.8 66.6 + - + +
324C ALA* 4.2 20.2 - - + -
330C ARG* 3.8 25.6 - - + -
333C TRP* 3.7 26.5 - + + -
334C VAL* 4.1 18.6 - - + -
337C ILE* 4.2 13.2 - - + -
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Residues in contact with CYS 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C ILE* 4.9 1.8 - - - -
160C VAL* 3.8 30.1 - - - -
287C ASP 3.8 0.3 - - - +
289C TYR* 2.9 45.9 + - - +
306C PHE* 1.3 77.4 - - - +
308C PHE* 1.3 69.9 + - - +
319C LEU* 3.8 25.6 - - + -
320C LYS 3.2 15.7 - - - +
321C MET* 4.0 17.0 - - + -
322C LEU* 5.4 0.2 - - - -
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Residues in contact with PHE 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C LEU* 4.0 7.0 - - + -
280C PHE* 3.9 11.0 - + - -
281C SER* 3.8 15.9 - - - +
283C PHE* 3.3 45.3 - + + -
286C SER* 4.3 11.2 - - - +
287C ASP 3.2 9.0 - - - +
288C ILE* 3.8 16.6 - - + -
306C PHE* 4.3 6.3 - + - -
307C CYS* 1.3 80.6 - - - +
309C LYS* 1.3 59.8 + - - +
310C PRO* 4.1 3.2 - - - +
319C LEU* 3.5 7.0 - - - +
320C LYS* 2.9 44.7 + - + +
322C LEU* 3.5 33.0 - - + -
337C ILE* 3.4 23.8 - - + -
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Residues in contact with LYS 309 (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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155C LEU* 3.9 23.8 - - + +
158C ILE* 5.7 5.6 - - + -
176C ASN* 4.6 14.1 + - - +
181C GLU* 4.1 20.1 + - - -
286C SER* 3.9 2.7 - - - -
287C ASP* 3.0 31.3 + - - +
289C TYR* 4.0 18.6 + - + +
307C CYS 4.3 0.4 + - - -
308C PHE* 1.3 73.8 - - - +
310C PRO* 1.3 83.8 + - + +
311C ASN* 4.6 0.4 - - - +
317C ARG* 3.8 38.9 - - + +
319C LEU* 3.9 21.1 - - + -
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Residues in contact with PRO 310 (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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176C ASN* 4.8 0.9 + - - -
285C ASN 3.3 10.8 - - - +
286C SER* 3.3 11.2 - - - +
308C PHE 4.1 1.8 - - - +
309C LYS* 1.3 105.3 + - + +
311C ASN* 1.3 70.8 + - - +
314C GLY* 4.1 18.4 - - - +
316C PRO 4.2 5.4 - - - +
317C ARG* 3.8 23.1 - - - +
318C ASP 3.6 24.5 - - - +
320C LYS* 5.1 10.5 - - - -
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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
------------------------------------------------------------
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