Contacts of the strand formed by residues 326 - 333 (chain C) in PDB entry 4X4R
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 PHE 326 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282C LYS* 3.5 42.0 - - + -
283C PHE* 3.3 20.9 - - - +
284C ARG* 4.4 18.2 - - + -
285C LYS* 4.0 1.1 - - - -
321C LYS 4.3 0.2 - - - +
322C ALA* 3.8 1.2 - - - -
323C SER* 2.9 40.7 + - - +
325C GLU* 1.3 118.7 - - + +
327C CYS* 1.3 63.8 + - - +
328C TYR* 4.2 14.4 - - + +
411C TYR* 6.2 5.6 - + - -
413C GLU* 6.0 0.7 - - - -
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Residues in contact with CYS 327 (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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281C VAL 3.4 5.2 - - - +
282C LYS* 3.5 4.3 - - - +
283C PHE* 2.8 55.1 + - + -
285C LYS* 3.6 34.8 - - - -
286C PRO* 4.1 9.4 - - - -
293C LEU* 4.3 9.4 - - - -
297C LEU* 4.3 9.4 - - + -
321C LYS 3.5 5.4 - - - +
322C ALA* 4.0 16.2 - - - -
326C PHE* 1.3 74.7 - - - +
328C TYR* 1.3 64.3 + - - +
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Residues in contact with TYR 328 (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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280C ALA* 4.6 12.3 - - + -
281C VAL 3.4 4.0 - - - -
282C LYS* 3.5 37.9 + - + -
297C LEU* 5.4 0.3 - - - +
320C PHE* 3.1 29.1 - - - +
321C LYS* 2.9 22.8 + - + +
323C SER* 4.3 13.1 + - - -
326C PHE* 4.2 17.4 - - + +
327C CYS* 1.3 79.1 - - - +
329C LEU* 1.3 64.1 + - - +
330C LEU* 3.9 8.3 - - + -
415C ILE* 5.6 1.3 - - + -
420C LEU* 5.4 0.7 - - + -
423C GLU* 2.5 40.7 + - + -
424C PRO* 3.3 26.1 - - + +
425C VAL* 3.5 30.1 - - + -
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Residues in contact with LEU 329 (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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280C ALA* 3.1 4.9 - - - -
281C VAL* 3.0 35.9 + - + +
283C PHE* 4.0 20.6 - - + -
297C LEU* 3.9 34.8 - - + +
300C ALA* 3.9 19.1 - - + -
301C SER* 4.3 7.0 - - - +
304C ILE* 3.7 27.1 - - + -
319C ALA 3.7 3.1 - - - +
320C PHE* 3.9 13.9 - - + -
328C TYR* 1.3 80.3 - - - +
330C LEU* 1.3 61.7 + - - +
331C PHE* 3.3 22.7 - - + -
408C ILE* 4.7 3.6 - - + -
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Residues in contact with LEU 330 (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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279C PHE 3.7 3.1 - - - +
280C ALA* 3.5 24.7 - - + -
318C SER* 3.3 4.0 - - - -
319C ALA* 2.5 51.4 + - + +
320C PHE* 4.5 5.4 - - - +
328C TYR* 4.0 5.8 - - + -
329C LEU* 1.3 70.9 - - - +
331C PHE* 1.3 71.7 + - - +
420C LEU* 4.7 1.3 - - + -
425C VAL* 4.0 32.1 - - + -
428C GLU* 3.7 31.2 - - + -
429C LEU* 4.1 21.5 - - + +
432C MET* 4.0 15.3 - - + -
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Residues in contact with PHE 331 (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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277C ALA 3.5 1.8 - - - +
278C VAL* 3.4 7.3 - - - +
279C PHE* 3.0 64.1 + + + +
281C VAL* 4.0 9.6 - - + -
301C SER* 3.5 31.4 - - - -
304C ILE* 3.4 33.0 - - + -
305C PHE* 4.1 7.9 - + - -
308C LEU* 3.9 18.6 - - + -
315C PRO* 6.2 0.7 - - + -
317C ARG 3.8 4.9 - - - +
318C SER* 3.9 11.0 - - - -
329C LEU* 3.3 40.4 - - + -
330C LEU* 1.3 79.5 - - - +
332C GLU* 1.3 61.2 - - - +
333C CYS* 4.9 1.1 - - - -
432C MET* 4.5 3.6 - - - +
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Residues in contact with GLU 332 (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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377A PHE* 4.6 3.6 - - - -
274C ARG* 2.5 39.5 + - - -
276C THR* 2.9 31.0 + - - +
277C ALA 3.3 2.7 - - - -
278C VAL* 3.9 8.5 - - + -
315C PRO* 3.5 3.6 - - - +
316C LEU* 2.7 51.3 + - + +
317C ARG* 3.3 15.3 + - - +
331C PHE* 1.3 76.5 - - - +
333C CYS* 1.3 60.7 + - - +
432C MET* 4.3 14.2 - - + +
433C MET* 3.8 21.6 - - - +
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Residues in contact with CYS 333 (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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276C THR* 3.3 7.9 - - - -
277C ALA* 2.8 42.0 + - + +
279C PHE* 4.1 16.2 - - - -
308C LEU* 4.1 31.0 - - - -
313C PHE* 3.4 15.7 - - - +
314C MET 3.6 3.6 - - - -
315C PRO* 4.0 13.9 - - - -
316C LEU* 4.7 0.4 - - - -
332C GLU* 1.3 83.6 - - - +
334C GLN* 1.3 65.0 + - - +
335C ILE 3.4 10.7 + - - +
385C PRO* 4.3 4.0 - - + -
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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