Contacts of the helix formed by residues 16 - 25 (chain B) in PDB entry 3DGR
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 ASP 16 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A PHE* 4.5 7.8 - - - +
195A TYR* 3.2 25.3 + - - +
196A ARG* 2.7 34.0 + - - -
219A ASP* 3.4 13.2 - - + +
15B THR* 1.3 79.6 + - - +
17B SER* 1.3 66.5 + - - +
18B TYR* 3.5 25.1 - - + -
19B LYS* 2.9 24.0 + - + +
150B THR* 2.6 25.4 + - - +
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Residues in contact with SER 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A ASP* 2.9 37.4 + - - +
221A VAL* 4.2 8.2 - - - +
241A SER* 3.7 9.0 - - - -
15B THR 3.2 3.5 + - - -
16B ASP* 1.3 69.2 - - - +
18B TYR* 1.3 57.7 + - - +
20B VAL* 2.9 37.1 + - - +
87B TYR* 5.0 1.6 - - - -
90B HIS* 2.7 39.1 + - - -
91B PHE* 3.2 9.7 - - - -
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Residues in contact with TYR 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A PHE* 4.3 7.9 - + + -
196A ARG* 2.9 27.0 + - - -
219A ASP* 3.0 26.4 + - - +
242A VAL 4.2 8.7 - - - +
244A ALA* 3.4 33.7 - - + +
245A ALA 4.0 6.5 - - - -
246A GLU* 3.8 23.0 + - + +
501A A12 3.3 30.4 + - - +
16B ASP* 3.0 25.9 + - + -
17B SER* 1.3 77.9 - - - +
19B LYS* 1.3 59.2 + - + +
20B VAL 3.1 0.2 - - - -
21B THR* 2.7 28.2 + - - -
22B HIS* 3.1 43.4 - + - -
91B PHE* 4.6 5.8 - - - -
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Residues in contact with LYS 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ARG* 3.7 15.7 - - - +
246A GLU* 2.7 30.5 + - - -
15B THR* 3.3 24.7 - - + +
16B ASP* 2.9 17.9 + - + +
18B TYR* 1.3 75.4 - - + +
20B VAL* 1.3 65.1 + - - +
21B THR 3.1 2.8 + - - -
22B HIS* 3.3 36.9 + - + +
23B TYR* 4.7 1.4 + - - -
146B ASN* 2.8 29.5 + - - +
147B TRP* 4.1 17.6 - - + -
149B GLU* 2.8 26.5 + - - -
150B THR* 3.6 17.3 - - - +
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Residues in contact with VAL 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B THR* 4.4 5.4 - - + -
17B SER 2.9 20.5 + - - +
19B LYS* 1.3 78.1 - - - +
21B THR* 1.3 55.5 + - - +
23B TYR* 3.3 24.6 - - - -
87B TYR* 3.5 39.9 - - + +
91B PHE* 4.1 7.2 - - + -
95B VAL* 4.1 17.4 - - + +
96B PHE* 3.9 32.5 - - + -
97B ASN 4.7 1.6 + - - +
147B TRP* 3.8 22.1 - - + -
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Residues in contact with THR 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A PRO* 4.2 13.4 - - + +
244A ALA 4.1 6.8 + - - -
269A PHE* 3.6 20.6 - - + -
18B TYR 2.7 19.8 + - - +
20B VAL* 1.3 76.5 - - - +
22B HIS* 1.3 61.4 + - - +
23B TYR* 3.1 9.6 + - - -
24B LYS* 3.1 22.2 + - - +
25B GLN* 3.2 19.4 + - - +
91B PHE* 4.5 8.7 - - + -
95B VAL* 3.6 37.7 - - + -
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Residues in contact with HIS 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A ALA 2.8 26.5 + - - -
246A GLU* 2.9 44.8 + - + +
248A SER* 5.1 0.2 + - - -
249A THR* 3.7 10.4 - - + +
18B TYR* 3.1 38.2 + + - -
19B LYS* 3.3 27.3 + - + +
21B THR* 1.3 72.5 - - - +
23B TYR* 1.3 57.1 + - - +
24B LYS 3.0 6.1 - - - -
25B GLN* 3.0 34.1 + - - +
26B TYR* 3.2 26.1 + - + +
143B TRP* 5.5 0.4 - - + -
146B ASN* 5.6 2.2 - - + +
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Residues in contact with TYR 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LYS 4.7 1.2 + - - -
20B VAL 3.3 25.6 - - - -
21B THR* 3.1 3.5 + - - -
22B HIS* 1.3 78.7 - - - +
24B LYS* 1.3 89.4 + - + +
25B GLN 3.3 1.4 + - - -
26B TYR* 4.4 3.2 + - - +
94B ASP 5.3 0.3 + - - -
95B VAL 2.9 24.3 + - - -
96B PHE 4.3 1.6 + - - -
97B ASN* 3.6 39.6 - - + +
142B TYR* 2.7 35.4 + - - +
143B TRP* 3.7 32.7 - + + +
147B TRP* 6.2 0.7 - + - -
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Residues in contact with LYS 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A HIS* 2.8 23.2 + - - -
268A GLN* 3.4 37.7 + - + +
269A PHE* 4.2 19.4 - - + -
21B THR* 3.1 10.4 + - - +
22B HIS 3.0 0.6 - - - -
23B TYR* 1.3 117.9 - - + +
25B GLN* 1.3 56.8 + - - +
26B TYR 3.7 1.6 - - - -
94B ASP 4.8 4.0 + - - -
95B VAL* 3.8 31.1 - - - +
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Residues in contact with GLN 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A ALA 3.0 25.2 + - - +
245A ALA* 3.1 17.5 - - - +
249A THR* 3.0 33.0 + - - +
253A TRP* 3.0 26.7 + - - -
264A HIS* 3.9 8.0 - - - -
265A ILE* 3.7 22.4 - - + +
269A PHE* 3.9 18.6 - - + -
21B THR* 3.2 29.3 + - - +
22B HIS* 3.0 16.5 + - - +
24B LYS* 1.3 82.4 - - - +
26B TYR* 1.3 64.1 + - - +
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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