Contacts of the helix formed by residues 296 - 311 (chain A) in PDB entry 3DC1
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 SER 296 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A SER* 4.9 1.0 + - - -
269A LEU 5.1 2.2 - - - -
270A ARG 5.3 1.4 + - - -
271A ILE* 4.1 2.0 - - - +
294A HIS 3.7 2.4 + - - -
295A PRO* 1.3 71.8 - - - +
297A THR* 1.3 64.7 + - - +
298A PHE* 3.7 5.7 + - - +
299A ASN* 3.3 28.5 + - - +
300A GLN* 3.2 21.1 + - - +
268B GLY 3.4 14.3 + - - -
269B LEU* 4.1 5.5 - - - -
270B ARG* 3.9 6.7 - - - +
296B SER* 5.0 5.2 - - - -
299B ASN* 2.8 27.3 + - - -
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Residues in contact with THR 297 (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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70A ARG* 3.3 25.8 - - + +
71A ALA* 3.8 7.2 - - - -
73A GLN 2.8 20.8 + - - +
75A SER* 2.6 35.8 + - - +
80A ILE* 4.1 11.4 - - + -
294A HIS* 3.0 7.3 + - - -
295A PRO 3.0 4.2 + - - -
296A SER* 1.3 70.3 - - - +
298A PHE* 1.3 65.9 + - - +
299A ASN 3.1 0.5 + - - -
300A GLN* 3.2 9.1 + - - +
301A LEU* 3.0 31.2 + - + +
268B GLY* 3.3 7.9 + - - -
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Residues in contact with PHE 298 (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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51A ALA* 4.3 11.7 - - + -
53A ILE* 4.4 4.9 - - + -
63A PHE* 3.6 30.3 - + - -
68A MET* 3.9 19.5 - - + -
71A ALA* 3.0 35.2 + - + +
72A LEU* 4.5 3.8 - - + -
296A SER* 3.7 2.5 - - - +
297A THR* 1.3 73.9 - - - +
299A ASN* 1.3 71.5 + - - +
301A LEU* 3.4 4.4 + - - +
302A MET* 3.1 44.9 + - + +
53B ILE* 4.8 3.4 - - + -
268B GLY 4.9 0.2 + - - -
269B LEU* 3.7 24.5 - - + -
298B PHE* 3.7 21.3 - + - -
299B ASN* 4.3 4.5 - - - -
302B MET* 4.2 13.9 - - + -
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Residues in contact with ASN 299 (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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269A LEU* 3.2 37.0 - - + +
271A ILE* 3.9 15.5 - - + -
296A SER* 3.3 18.1 + - - +
297A THR 3.2 1.0 - - - -
298A PHE* 1.3 88.5 - - - +
300A GLN* 1.3 65.8 + - - +
301A LEU 3.2 0.2 - - - -
302A MET* 3.4 10.0 + - - +
303A ILE* 3.0 27.9 + - - +
296B SER* 2.8 28.1 + - - -
298B PHE* 4.5 0.4 - - - -
299B ASN* 3.1 20.7 + - - +
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Residues in contact with GLN 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A SER* 4.6 1.2 + - - -
79A GLY* 3.3 7.0 - - - -
80A ILE* 2.9 47.1 + - + +
83A LEU* 3.4 25.5 - - + +
113A VAL* 3.9 3.1 - - + +
271A ILE* 3.4 19.7 - - + -
294A HIS* 4.5 2.8 - - - +
295A PRO* 2.8 48.1 + - + +
296A SER 3.2 5.7 + - - -
297A THR* 3.2 8.9 + - - +
299A ASN* 1.3 76.7 - - - +
301A LEU* 1.3 54.0 + - - +
303A ILE* 3.6 2.6 - - - +
304A SER* 2.6 38.1 + - - -
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Residues in contact with LEU 301 (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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63A PHE* 3.7 13.2 - - + -
67A MET* 3.8 28.9 - - + -
70A ARG* 4.0 27.4 - - - +
71A ALA* 4.1 18.4 - - + -
80A ILE* 3.4 20.9 - - + -
82A GLU* 4.3 6.5 - - + +
297A THR* 3.0 29.1 + - + +
298A PHE 3.6 9.2 - - - +
300A GLN* 1.3 76.6 - - - +
302A MET* 1.3 63.1 + - - +
304A SER* 4.6 5.2 - - - -
305A GLN* 3.1 40.8 + - + +
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Residues in contact with MET 302 (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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53A ILE* 3.5 28.3 - - + -
61A ILE* 3.3 18.3 - - + +
63A PHE* 3.9 9.4 - - + -
269A LEU* 3.8 10.8 - - + -
298A PHE* 3.1 42.5 + - + +
299A ASN* 3.4 18.8 - - - +
300A GLN 3.2 0.2 - - - -
301A LEU* 1.3 77.0 - - - +
303A ILE* 1.3 61.7 + - - +
306A LEU* 3.3 17.7 + - - +
48B PHE* 3.8 40.1 - - + -
298B PHE* 4.2 18.8 - - + -
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Residues in contact with ILE 303 (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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83A LEU* 3.9 14.4 - - + -
261A PHE* 4.5 13.9 - - + -
265A ILE* 3.9 29.6 - - + -
266A SER* 5.5 1.1 - - - +
269A LEU* 4.2 15.7 - - + -
271A ILE* 3.9 31.0 - - + +
299A ASN 3.0 17.7 + - - +
300A GLN* 3.8 3.1 - - - +
302A MET* 1.3 78.6 - - - +
304A SER* 1.3 65.8 + - - +
306A LEU* 3.0 8.7 + - + +
307A LEU* 3.0 47.3 + - + +
48B PHE* 4.2 8.5 - - + -
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Residues in contact with SER 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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80A ILE* 4.2 6.3 - - - -
82A GLU* 3.6 9.7 - - - +
83A LEU* 3.4 26.6 + - - -
300A GLN 2.6 22.7 + - - -
301A LEU* 4.0 6.5 - - - -
303A ILE* 1.3 76.7 - - - +
305A GLN* 1.3 64.4 + - - +
307A LEU* 3.1 7.7 + - - +
308A HIS* 2.8 50.7 + - - -
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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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61A ILE* 4.2 20.1 - - + +
62A GLN 4.0 18.0 + - - +
63A PHE* 3.3 20.4 - - - -
67A MET* 4.2 14.2 - - - +
301A LEU* 3.1 34.1 + - + +
302A MET 4.3 1.6 - - - +
304A SER* 1.3 77.2 - - - +
306A LEU* 1.3 60.2 + - - +
308A HIS* 4.2 6.4 - - - +
309A GLU* 3.2 24.3 + - - +
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Residues in contact with LEU 306 (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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55A VAL* 3.9 34.5 - - + -
61A ILE* 4.2 5.6 - - + +
265A ILE* 4.5 13.7 - - + -
302A MET 3.3 14.0 + - - +
303A ILE* 3.0 10.5 + - - +
305A GLN* 1.3 75.6 - - - +
307A LEU* 1.3 69.5 - - + +
309A GLU* 3.6 3.8 + - - +
310A TRP* 3.0 62.7 + - + +
47B PRO* 3.9 25.6 - - + -
48B PHE* 4.0 17.3 - - + -
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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
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83A LEU* 4.0 14.6 - - + -
86A TRP* 3.4 43.4 + - + -
261A PHE* 4.7 9.9 - - + -
265A ILE* 4.3 8.1 - - + -
303A ILE* 3.0 41.7 + - + +
304A SER* 3.6 5.8 - - - +
306A LEU* 1.3 93.4 - - + +
308A HIS* 1.3 54.6 + - - +
309A GLU 3.2 0.2 - - - -
310A TRP* 4.4 6.1 - - + -
311A GLY* 2.7 34.1 + - - +
315A PHE* 4.2 26.0 - - + -
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Residues in contact with HIS 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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82A GLU* 3.1 37.9 + - + +
85A SER* 5.2 2.0 + - - -
86A TRP* 3.3 31.1 - + + +
304A SER* 2.8 43.8 + - - +
305A GLN* 4.6 5.6 - - - +
307A LEU* 1.3 75.2 - - + +
309A GLU* 1.3 60.2 + - - +
311A GLY* 3.8 7.8 + - - -
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Residues in contact with GLU 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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58A GLY* 5.9 1.1 - - - -
59A LYS* 3.5 54.6 - - + +
305A GLN 3.2 20.2 + - - +
306A LEU* 3.8 3.6 - - - +
307A LEU 3.2 0.4 - - - -
308A HIS* 1.3 77.3 - - - +
310A TRP* 1.3 67.4 + - + +
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Residues in contact with TRP 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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55A VAL* 4.7 4.2 - - + +
56A GLU 4.8 5.2 - - - -
57A ASN* 3.4 22.9 + - + -
58A GLY* 4.7 7.1 - - - -
265A ILE* 5.6 2.2 - - + -
306A LEU* 3.0 51.0 + - + +
307A LEU* 3.9 7.9 - - + +
309A GLU* 1.3 81.2 - - + +
311A GLY* 1.3 55.2 + - - +
313A GLU 2.3 23.6 - - - +
314A GLY* 3.5 23.2 + - - -
315A PHE* 3.7 28.9 - + - +
318A HIS* 3.2 51.4 - + + -
47B PRO* 3.9 19.3 - - + -
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Residues in contact with GLY 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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86A TRP* 3.8 8.7 - - - -
307A LEU 2.7 20.6 + - - -
308A HIS* 3.8 8.0 + - - -
309A GLU 3.4 2.4 - - - -
310A TRP* 1.3 79.7 - - - +
312A GLU* 1.3 69.4 + - - +
313A GLU 3.1 2.1 - - - +
315A PHE* 3.2 14.0 + - - +
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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
------------------------------------------------------------
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