Contacts of the helix formed by residues 302 - 314 (chain A) in PDB entry 3UGM
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 302 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A ASN* 3.4 3.6 - - - +
301A ASN* 1.3 79.0 - - - +
303A GLY* 1.3 70.2 + - - +
304A LYS 3.4 1.3 - - - -
305A GLN* 2.7 19.3 + - - -
306A ALA* 2.8 17.6 + - - -
335A ASP* 4.7 0.4 - - - +
336A GLY 4.7 10.5 - - - +
337A GLY 5.7 0.4 - - - -
338A LYS 6.1 0.2 - - - -
0B T 4.1 4.3 - - - -
1B G 3.2 26.1 + - - -
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Residues in contact with GLY 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A GLY 4.7 1.1 - - - -
270A THR* 4.9 0.2 - - - -
271A ALA* 3.8 9.6 - - - -
297A ILE 3.6 7.6 + - - +
298A ALA* 3.3 26.0 - - - -
300A ASN* 3.2 7.7 + - - +
301A ASN 2.8 9.0 + - - -
302A GLY* 1.3 84.5 - - - +
304A LYS* 1.3 51.5 + - - -
306A ALA* 3.2 3.3 + - - +
307A LEU* 2.8 33.2 + - - +
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Residues in contact with LYS 304 (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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270A THR* 3.7 42.0 + - + +
271A ALA* 3.9 6.7 - - - +
273A GLU* 5.4 6.1 + - - +
274A ALA* 3.6 29.8 - - + -
302A GLY 2.9 1.2 + - - -
303A GLY* 1.3 71.5 - - - +
305A GLN* 1.3 67.5 + - + +
307A LEU* 3.3 3.4 - - - +
308A GLU* 2.8 47.7 + - + +
0B T 3.2 18.5 + - - +
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Residues in contact with GLN 305 (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 GLY* 2.7 14.5 + - - +
304A LYS* 1.3 76.8 - - + +
306A ALA* 1.3 67.2 + - - +
307A LEU 3.0 0.9 - - - -
308A GLU* 2.9 6.6 + - - -
309A THR* 2.7 30.6 + - - -
338A LYS* 2.9 40.2 + - + +
-1B A 4.6 1.2 + - - -
0B T 3.4 40.1 + - - +
1B G 3.3 18.4 + - - +
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Residues in contact with ALA 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ILE* 3.6 17.3 - - - +
300A ASN* 5.7 1.1 - - - +
302A GLY* 2.8 18.7 + - - +
303A GLY 3.4 7.6 - - - +
305A GLN* 1.3 72.7 - - - +
307A LEU* 1.3 67.1 + - - +
309A THR* 3.3 4.1 + - - -
310A VAL* 3.0 23.5 + - - +
332A ALA* 4.0 20.0 - - + +
334A HIS 5.6 0.7 - - - +
337A GLY* 4.5 11.9 - - - +
338A LYS* 4.4 13.9 - - - +
341A LEU* 4.7 0.6 - - - +
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Residues in contact with LEU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A ALA* 4.4 2.0 - - + +
274A ALA* 4.1 22.2 - - + +
275A VAL* 3.7 19.1 - - + -
278A SER* 5.0 4.3 - - - +
282A LEU* 4.1 35.2 - - + -
289A LEU* 6.1 0.7 - - + -
294A VAL* 5.5 3.4 - - + -
297A ILE* 4.5 16.9 + - + -
298A ALA* 3.7 34.1 - - + -
303A GLY 2.8 13.5 + - - +
304A LYS* 3.3 10.5 - - - +
306A ALA* 1.3 77.2 - - - +
308A GLU* 1.3 68.1 + - + +
310A VAL* 3.0 15.2 + - + +
311A GLN* 3.3 11.4 + - + +
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Residues in contact with GLU 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ALA* 4.6 13.9 - - - +
278A SER* 4.5 17.7 + - - -
304A LYS* 2.8 46.6 + - + +
305A GLN* 2.9 4.4 + - - +
307A LEU* 1.3 74.9 - - - +
309A THR* 1.3 64.3 + - - +
311A GLN* 3.5 11.0 + - - +
312A ARG* 3.5 20.4 + - - +
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Residues in contact with THR 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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305A GLN* 2.7 22.7 + - - -
306A ALA* 3.5 5.4 - - - -
308A GLU* 1.3 70.7 - - - +
310A VAL* 1.3 56.5 + - - +
312A ARG* 2.5 60.6 + - - +
313A LEU* 2.8 23.5 + - + -
338A LYS* 3.5 24.8 + - - +
341A LEU* 3.6 28.3 - - + -
342A GLU* 4.9 3.8 - - + +
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Residues in contact with VAL 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A LEU* 6.1 0.7 - - + -
288A ASN* 5.8 0.9 - - - +
289A LEU* 4.5 29.8 - - + -
297A ILE* 4.6 10.5 - - + -
306A ALA 3.0 9.2 + - - +
307A LEU* 3.0 10.7 + - + +
309A THR* 1.3 76.9 - - - +
311A GLN* 1.3 63.6 + - + +
313A LEU 4.3 1.6 - - - +
314A LEU* 2.9 38.9 + - + +
328A VAL* 3.9 20.2 - - + -
329A VAL* 5.0 3.6 - - + -
332A ALA* 3.9 19.7 - - + -
341A LEU* 3.8 24.0 - - + -
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Residues in contact with GLN 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A SER* 3.2 18.9 + - - -
281A ALA* 2.8 32.1 + - - +
282A LEU* 3.5 14.6 - - + -
286A PRO* 5.4 0.4 - - - +
288A ASN* 2.5 42.2 + - - +
307A LEU* 3.3 8.8 + - + +
308A GLU* 3.9 13.0 - - - +
309A THR 3.1 0.8 - - - -
310A VAL* 1.3 82.1 - - + +
312A ARG* 1.3 57.8 + - - +
314A LEU 4.9 0.2 - - - -
315A PRO* 4.8 8.0 - - - +
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Residues in contact with ARG 312 (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 GLU* 3.5 10.1 + - - +
309A THR* 2.5 60.6 + - - +
311A GLN* 1.3 74.3 - - - +
313A LEU* 1.3 79.7 + - + +
314A LEU 3.8 0.9 - - - -
315A PRO* 4.3 7.5 - - - +
316A VAL* 4.5 7.4 - - - +
338A LYS* 4.9 4.9 - - - +
342A GLU* 3.1 28.5 + - - +
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Residues in contact with LEU 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A THR* 2.8 31.2 + - + +
310A VAL* 3.8 2.2 - - - -
312A ARG* 1.3 112.4 - - + +
314A LEU* 1.3 60.8 + - - +
315A PRO* 3.5 1.1 - - - -
316A VAL* 4.2 20.4 - - + -
317A LEU* 2.8 43.4 + - + +
328A VAL* 5.4 0.7 - - - -
341A LEU* 4.9 11.0 - - + +
342A GLU* 4.8 9.6 - - + -
345A GLN* 4.5 15.7 - - + -
346A ARG* 4.4 20.2 - - - +
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Residues in contact with LEU 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ASN* 4.5 17.0 - - - +
289A LEU* 3.8 28.0 - - + -
310A VAL* 2.9 22.2 + - + +
311A GLN* 5.4 0.4 - - - -
313A LEU* 1.3 75.7 - - - +
315A PRO* 1.4 71.9 - - + +
317A LEU* 3.1 5.0 + - - +
318A CYS* 3.0 39.9 + - - -
324A THR 3.9 5.2 - - - +
325A PRO* 4.0 16.2 - - + +
328A VAL* 3.5 34.8 - - + -
329A VAL* 5.1 1.8 - - + -
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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