Contacts of the helix formed by residues 308 - 323 (chain A) in PDB entry 1DGD
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 PRO 308 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A TYR* 5.0 1.3 - - + -
75A LEU* 3.7 36.3 - - + -
76A ASP 3.8 16.4 - - - +
78A LEU* 3.5 39.5 - - + -
84A SER* 3.8 12.8 - - - +
86A PRO* 3.9 7.5 - - + +
87A VAL* 4.6 1.1 - - + -
306A SER 3.8 3.6 - - - +
307A ASP* 1.3 88.0 - - + +
309A LEU* 1.3 64.2 + - - +
311A ALA* 3.1 6.5 + - + +
312A ALA* 2.8 24.3 + - - +
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Residues in contact with LEU 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ILE* 4.4 16.2 - - + +
71A TYR* 4.0 13.2 - - + -
72A ALA* 3.7 34.5 - - + +
75A LEU 3.9 8.1 + - - +
76A ASP* 3.6 20.1 + - + +
278A LEU* 4.3 12.6 - - + -
308A PRO* 1.3 78.3 - - - +
310A PRO* 1.3 76.1 - - + +
312A ALA* 3.2 6.5 + - - +
313A VAL* 3.1 39.8 + - + +
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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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76A ASP 4.6 1.3 - - - +
108A LEU 5.5 0.9 - - - +
278A LEU* 4.6 10.1 - - + -
279A PRO 4.0 21.5 - - - +
280A LEU* 3.4 22.0 - - + +
304A HIS* 5.6 6.5 - - + +
307A ASP* 3.8 23.8 - - + +
308A PRO 3.8 1.3 - - - -
309A LEU* 1.3 102.2 - - + +
311A ALA* 1.3 63.2 + - - +
313A VAL* 3.1 8.6 + - + +
314A GLY 3.0 18.5 + - - -
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Residues in contact with ALA 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PRO* 3.8 26.5 - - - +
87A VAL* 3.9 10.8 - - + +
90A LEU* 3.6 21.1 - - + +
107A LEU* 4.3 6.3 - - + -
280A LEU* 4.5 4.1 - - + +
307A ASP 3.4 18.5 + - - +
308A PRO 3.1 4.4 + - - +
310A PRO* 1.3 79.1 - - - +
312A ALA* 1.3 63.4 + - - +
314A GLY 3.1 1.7 + - - -
315A LEU* 3.0 22.5 + - - +
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Residues in contact with ALA 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A VAL* 4.0 8.4 - - + +
71A TYR* 3.6 44.0 - - + -
86A PRO* 3.7 11.1 - - + +
308A PRO 2.8 15.4 + - - +
309A LEU 3.2 10.1 - - - +
311A ALA* 1.3 71.7 - - - +
313A VAL* 1.3 63.5 + - + +
315A LEU* 3.3 6.7 + - - +
316A ARG* 3.0 22.5 + - - +
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Residues in contact with VAL 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ILE* 4.1 23.7 - - + +
67A VAL* 4.3 11.2 - - + -
68A ILE* 3.8 26.7 - - + -
275A GLY* 4.2 19.3 - - - +
278A LEU* 4.4 13.9 - - + -
280A LEU* 5.7 0.4 - - + -
309A LEU* 3.1 26.8 + - + +
310A PRO* 3.4 9.0 - - + +
312A ALA* 1.3 75.2 - - + +
314A GLY* 1.3 66.9 + - - +
316A ARG* 3.2 3.5 + - - +
317A VAL* 2.9 26.1 + - + +
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Residues in contact with GLY 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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90A LEU* 4.3 7.4 - - - -
274A LEU* 3.8 16.1 - - - +
280A LEU* 3.5 24.8 - - - +
310A PRO 3.0 11.7 + - - -
311A ALA 3.1 1.3 + - - -
313A VAL* 1.3 77.1 - - - +
315A LEU* 1.3 62.7 + - - +
317A VAL* 3.1 4.4 + - - +
318A LEU* 3.0 24.8 + - - +
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Residues in contact with LEU 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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86A PRO* 4.5 10.1 - - + +
89A ASP* 3.4 51.6 - - + +
90A LEU* 3.9 18.6 - - + +
93A ARG* 3.9 33.2 - - + +
311A ALA 3.0 12.3 + - - +
312A ALA* 3.5 9.4 - - - +
313A VAL 3.2 0.2 - - - -
314A GLY* 1.3 75.2 - - - +
316A ARG* 1.3 64.1 + - - +
318A LEU* 2.9 16.2 + - + +
319A ASP* 2.9 20.6 + - - +
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Residues in contact with ARG 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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63A GLU* 2.9 54.5 + - + +
64A ILE* 4.2 6.1 - - + -
66A SER* 4.6 6.5 + - - -
67A VAL* 3.9 22.8 - - + +
70A GLU* 3.7 21.4 + - - -
312A ALA 3.0 13.7 + - - +
313A VAL 3.2 6.7 + - - +
315A LEU* 1.3 75.5 - - - +
317A VAL* 1.3 62.4 + - - +
319A ASP* 3.3 18.7 + - - -
320A VAL* 3.0 32.6 + - + +
323A ARG* 5.4 1.8 - - - +
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Residues in contact with VAL 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A VAL* 4.4 4.9 - - + -
57A LEU* 4.3 11.2 - - + -
64A ILE* 3.6 19.1 - - + -
249A VAL* 4.4 6.7 - - + -
273A THR 4.2 12.8 - - - +
274A LEU* 3.9 17.5 - - - +
276A ALA* 3.5 28.7 - - + -
313A VAL* 2.9 22.5 + - + +
314A GLY 3.1 7.5 + - - +
316A ARG* 1.3 77.9 - - - +
318A LEU* 1.3 62.5 + - + +
320A VAL* 3.2 3.3 + - - +
321A VAL* 3.0 32.4 + - + +
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Residues in contact with LEU 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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90A LEU* 3.7 30.1 - - + -
93A ARG* 3.9 24.0 - - + +
94A LEU* 4.4 12.3 - - + -
97A ILE* 4.1 8.7 - - + -
249A VAL* 4.1 26.2 - - + -
255A MET* 3.9 23.3 - - + -
256A PHE* 5.8 0.7 - - + -
274A LEU* 4.5 10.1 - - + -
314A GLY 3.0 9.2 + - - +
315A LEU* 2.9 7.3 + - - +
317A VAL* 1.3 74.9 - - + +
319A ASP* 1.3 63.7 + - - +
321A VAL* 3.4 3.7 + - - +
322A GLN* 3.0 39.0 + - - +
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Residues in contact with ASP 319 (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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93A ARG* 2.3 45.0 + - - +
315A LEU* 2.9 19.9 + - - +
316A ARG* 3.6 26.8 + - - +
317A VAL 3.2 0.2 - - - -
318A LEU* 1.3 76.6 - - - +
320A VAL* 1.3 59.1 + - + +
322A GLN* 3.8 1.8 - - - +
323A ARG* 2.9 37.0 + - + +
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Residues in contact with VAL 320 (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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57A LEU* 3.9 27.6 - - + -
61A HIS* 4.1 15.0 - - + +
63A GLU* 3.9 22.9 - - + -
316A ARG* 3.0 33.0 + - + +
317A VAL 3.8 3.4 - - - +
318A LEU 3.2 0.2 - - - -
319A ASP* 1.3 75.2 - - - +
321A VAL* 1.3 60.5 + - - +
323A ARG* 4.1 14.1 - - - +
324A ASP* 2.8 49.3 + - - +
326A LEU* 4.3 3.6 - - + -
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Residues in contact with VAL 321 (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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56A VAL* 5.3 1.6 - - + -
57A LEU* 4.2 17.0 - - + -
249A VAL* 4.0 25.6 - - + +
255A MET* 4.1 21.1 - - + -
317A VAL* 3.0 19.7 + - + +
318A LEU* 3.7 5.6 - - - +
320A VAL* 1.3 74.6 - - - +
322A GLN* 1.3 64.0 + - - +
325A GLY* 3.2 2.1 + - - -
326A LEU* 3.0 41.9 + - + -
327A VAL* 4.1 25.1 + - + +
411A LEU* 4.7 5.4 - - + -
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Residues in contact with GLN 322 (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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93A ARG* 3.1 39.8 + - - +
97A ILE* 4.0 20.5 - - + +
255A MET* 4.6 12.3 - - + +
318A LEU* 3.0 20.7 + - - +
319A ASP* 3.8 3.1 - - - +
321A VAL* 1.3 75.2 - - + +
323A ARG* 1.3 66.7 + - - +
325A GLY* 2.9 14.6 + - - -
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Residues in contact with ARG 323 (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 HIS* 5.6 0.8 - - - -
63A GLU* 2.5 39.0 + - - +
316A ARG* 5.4 1.8 - - - +
319A ASP* 2.9 26.2 + - + +
320A VAL* 3.9 17.1 - - - +
322A GLN* 1.3 75.4 - - - +
324A ASP* 1.3 106.6 + - - +
325A GLY 3.3 2.6 + - - -
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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