Contacts of the helix formed by residues 307 - 318 (chain A) in PDB entry 4UEL
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 GLN 307 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302A LEU* 2.8 23.8 + - + +
305A HIS* 3.5 27.6 + - + +
306A GLN* 1.3 82.2 + - - +
308A LEU* 1.3 63.4 + - - +
309A ILE 3.4 1.8 - - - -
310A PRO* 3.6 12.7 - - - +
311A LEU* 3.1 33.2 + - + +
299C PRO* 5.4 2.6 - - - +
300C ILE* 3.5 32.1 - - + +
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Residues in contact with LEU 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A LEU* 3.7 44.4 - - + +
302A LEU* 3.4 22.2 + - + -
303A ALA* 4.0 12.3 - - + +
307A GLN* 1.3 78.6 - - - +
309A ILE* 1.3 61.7 + - - +
311A LEU* 3.5 2.3 + - + +
312A VAL* 3.1 37.4 + - + +
288C LEU* 5.5 1.8 - - + -
291C VAL* 5.1 5.6 - - + -
292C LEU* 5.0 4.3 - - + -
377C PHE* 4.8 3.8 - - + -
378C ALA* 3.9 28.5 - - + +
381C MET* 4.1 20.9 - - + -
382C GLN* 2.8 8.8 + - - +
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Residues in contact with ILE 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A LEU* 1.3 73.2 - - - +
310A PRO* 1.4 77.6 - - + +
312A VAL* 3.2 4.7 + - - +
313A GLU* 3.2 41.1 + - + +
375C GLU 5.7 0.4 - - - +
378C ALA* 3.8 18.6 - - + +
379C LYS* 3.8 26.7 - - + +
382C GLN* 3.1 34.4 + - + +
383C ASN* 4.5 4.7 - - - +
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Residues in contact with PRO 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A GLN 3.6 22.9 - - - +
307A GLN* 3.6 17.7 - - - +
309A ILE* 1.4 98.0 - - + +
311A LEU* 1.3 66.8 + - + +
313A GLU* 3.4 9.0 + - + +
314A LYS* 3.1 27.8 + - + +
382C GLN* 3.9 2.0 - - - +
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Residues in contact with LEU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A LEU* 3.7 33.2 - - + -
307A GLN* 3.1 24.8 + - + +
308A LEU* 4.0 3.6 - - - +
309A ILE 3.2 0.2 - - - -
310A PRO* 1.3 82.9 - - + +
312A VAL* 1.3 61.8 + - - +
314A LYS* 3.4 25.6 + - + +
315A ALA* 3.3 17.5 + - - +
291C VAL* 3.7 27.7 - - + +
296C ILE* 3.7 26.9 - - + +
297C MET* 4.3 16.6 - - + -
300C ILE* 4.4 10.5 - - + -
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Residues in contact with VAL 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A LEU* 3.1 24.4 + - + +
309A ILE* 3.2 5.1 + - - +
311A LEU* 1.3 77.4 - - - +
313A GLU* 1.3 60.8 + - + +
315A ALA* 3.4 4.3 + - - +
316A LYS* 3.0 27.4 + - + +
287C ASP* 6.0 2.2 - - - +
288C LEU* 5.1 4.3 - - + -
291C VAL* 4.0 20.1 - - + +
374C VAL* 4.8 16.6 - - + +
375C GLU* 4.4 31.0 - - + +
378C ALA* 3.9 18.2 - - + -
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Residues in contact with GLU 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A ILE* 3.2 30.7 + - + +
310A PRO* 3.8 9.2 - - - +
312A VAL* 1.3 76.2 - - + +
314A LYS* 1.3 55.4 + - - +
316A LYS* 3.4 12.1 - - + +
317A GLU* 2.7 48.6 + - + +
375C GLU* 4.9 14.5 - - + +
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Residues in contact with LYS 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A PRO* 3.1 17.1 + - + +
311A LEU* 3.5 29.7 - - + +
312A VAL 3.2 0.4 - - - -
313A GLU* 1.3 72.8 - - - +
315A ALA* 1.3 60.0 + - - +
317A GLU* 3.2 11.3 + - - +
318A LYS* 2.9 46.9 + - + +
296C ILE* 3.7 39.9 + - + +
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Residues in contact with ALA 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A LEU 3.3 3.8 + - - +
312A VAL 3.8 2.5 - - - +
314A LYS* 1.3 78.2 - - - +
316A LYS* 1.3 61.0 + - - +
318A LYS* 3.9 11.6 + - - +
319A GLN* 3.2 26.9 - - - +
287C ASP* 4.8 9.0 - - + +
290C SER* 3.6 23.0 + - - +
291C VAL* 3.3 37.9 - - + +
296C ILE* 5.7 1.4 - - + +
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Residues in contact with LYS 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A VAL* 3.0 17.5 + - + +
313A GLU* 3.4 17.7 - - + +
314A LYS 3.1 0.2 - - - -
315A ALA* 1.3 74.5 - - - +
317A GLU* 1.3 66.8 + - + +
319A GLN* 3.1 22.9 + - - +
320A ASN* 3.6 11.3 - - - +
287C ASP* 6.0 1.8 - - - +
375C GLU* 2.7 35.1 + - - +
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Residues in contact with GLU 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A GLU* 2.7 32.8 + - + +
314A LYS* 3.7 10.2 - - - +
316A LYS* 1.3 73.0 - - + +
318A LYS* 1.3 59.1 + - + +
319A GLN 3.1 4.7 + - - -
320A ASN* 3.2 26.7 + - - +
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Residues in contact with LYS 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A LYS* 2.9 39.5 + - + +
315A ALA* 4.2 8.5 - - - +
316A LYS 3.2 0.8 - - - -
317A GLU* 1.3 76.2 - - + +
319A GLN* 1.3 73.5 + - - +
290C SER* 5.1 8.5 - - - -
295C GLU* 5.4 5.9 + - - -
296C ILE* 5.1 19.0 - - + +
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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