Contacts of the helix formed by residues 1 - 19 (chain X) in PDB entry 3CR4
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 1 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0X MET* 1.3 75.8 - - - +
2X GLU* 1.3 58.1 + - - +
3X LEU* 3.4 9.8 + - - +
4X GLU* 3.0 38.5 + - - +
5X LYS* 2.9 30.0 + - - +
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Residues in contact with GLU 2 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1X SER* 1.3 70.3 - - - +
3X LEU* 1.3 61.1 + - - +
5X LYS* 2.7 38.5 + - - +
6X ALA* 2.8 30.8 + - - +
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Residues in contact with LEU 3 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1X SER* 3.3 8.4 + - - +
2X GLU* 1.3 77.9 - - - +
4X GLU* 1.3 58.9 + - + +
6X ALA* 3.1 9.8 + - + +
7X VAL* 3.0 42.1 + - + +
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Residues in contact with GLU 4 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0X MET* 3.4 37.2 - - + +
1X SER* 3.0 39.0 + - - +
3X LEU* 1.3 78.9 - - + +
5X LYS* 1.3 60.8 + - - +
7X VAL* 3.5 8.2 + - - +
8X VAL* 3.3 18.0 + - - +
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Residues in contact with LYS 5 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0X MET* 3.3 38.5 + - + +
1X SER 2.9 16.3 + - - +
2X GLU* 2.7 36.1 + - - +
4X GLU* 1.3 73.9 - - - +
6X ALA* 1.3 59.9 + - - +
8X VAL* 3.2 14.1 - - + +
9X ALA* 3.0 27.7 + - - +
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Residues in contact with ALA 6 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2X GLU 2.8 17.7 + - - +
3X LEU* 3.1 12.5 + - + +
5X LYS* 1.3 74.9 - - - +
7X VAL* 1.3 65.0 + - - +
9X ALA* 3.3 8.3 + - - +
10X LEU* 3.1 31.4 + - + +
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Residues in contact with VAL 7 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3X LEU* 3.0 32.7 + - + +
4X GLU* 3.6 11.0 - - - +
6X ALA* 1.3 75.5 - - - +
8X VAL* 1.3 65.1 + - + +
10X LEU* 3.2 21.8 + - + +
11X ILE* 3.4 26.9 + - + +
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Residues in contact with VAL 8 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0X MET* 3.8 16.8 - - + -
4X GLU 3.3 12.7 + - - +
5X LYS* 3.2 20.4 - - + +
7X VAL* 1.3 80.7 - - + +
9X ALA* 1.3 55.7 + - - +
11X ILE* 3.1 14.5 + - + +
12X ASP* 2.7 52.2 + - - +
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Residues in contact with ALA 9 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5X LYS 3.0 16.8 + - - +
6X ALA* 3.5 10.5 - - - +
7X VAL 3.3 0.2 - - - -
8X VAL* 1.3 78.5 - - + +
10X LEU* 1.3 59.1 + - + +
12X ASP* 3.7 9.7 - - - +
13X VAL* 3.1 30.7 + - - +
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Residues in contact with LEU 10 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6X ALA* 3.1 22.6 + - + +
7X VAL* 3.4 15.7 - - + +
8X VAL 3.2 0.2 - - - -
9X ALA* 1.3 77.4 - - + +
11X ILE* 1.3 62.5 + - + +
13X VAL* 3.4 11.5 - - + +
14X PHE* 3.4 17.0 + - - +
70X PHE* 4.6 1.9 - - - -
73X PHE* 3.5 14.0 - - + -
74X MET* 3.9 34.5 - - + -
77X VAL* 4.0 31.2 - - + -
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Residues in contact with ILE 11 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7X VAL* 3.4 28.0 - - + +
8X VAL* 3.1 15.4 + - + +
10X LEU* 1.3 75.9 - - + +
12X ASP* 1.3 68.8 - - - +
14X PHE* 3.5 1.4 + - - +
15X HIS* 3.0 50.0 + - + +
70X PHE* 4.0 26.2 - - + -
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Residues in contact with ASP 12 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8X VAL* 2.7 37.7 + - - +
9X ALA* 3.7 8.9 - - - +
11X ILE* 1.3 78.7 - - - +
13X VAL* 1.3 57.8 + - - +
15X HIS* 3.3 3.5 + - - +
16X GLN* 2.9 46.5 + - - +
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Residues in contact with VAL 13 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9X ALA 3.1 15.5 + - - +
10X LEU* 3.4 18.4 - - + +
12X ASP* 1.3 72.9 - - - +
14X PHE* 1.3 71.2 + - - +
16X GLN* 3.4 12.2 + - + -
17X TYR* 3.3 30.2 - - + -
35X LEU* 3.9 7.8 - - + +
39X GLU* 3.7 37.5 - - + +
73X PHE* 3.8 18.6 - - + -
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Residues in contact with PHE 14 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10X LEU 3.4 12.9 + - - +
11X ILE 3.8 4.3 - - - +
12X ASP 3.3 0.4 - - - -
13X VAL* 1.3 84.9 - - - +
15X HIS* 1.3 75.0 + + - +
17X TYR* 3.3 1.2 + - - -
18X SER* 2.8 51.0 + - - -
25X HIS* 3.2 32.1 - - - -
26X LYS* 4.1 0.2 - - - -
27X LEU* 3.7 25.3 - - + +
35X LEU* 4.6 4.9 - - - -
68X CYS 3.8 4.3 - - - -
69X ASP 3.7 18.8 - - - -
70X PHE* 3.6 31.6 - + + -
73X PHE* 3.5 33.4 - + + -
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Residues in contact with HIS 15 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11X ILE* 3.0 40.4 + - + +
12X ASP* 3.3 4.9 + - - +
14X PHE* 1.3 93.5 - + + +
16X GLN* 1.3 66.3 + - - +
17X TYR 3.0 2.3 + - - -
18X SER* 3.5 16.4 - - - -
19X GLY* 3.5 17.4 + - - -
24X LYS 4.4 7.0 - - - -
25X HIS* 4.5 15.6 + + - +
70X PHE* 4.8 5.4 - + + -
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Residues in contact with GLN 16 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12X ASP* 2.9 40.1 + - - +
13X VAL* 3.4 18.7 + - + +
15X HIS* 1.3 79.1 - - - +
17X TYR* 1.3 70.4 + - + +
20X ARG* 3.1 29.9 + - - +
39X GLU* 6.3 0.2 - - - -
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Residues in contact with TYR 17 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13X VAL* 3.3 17.0 - - + -
14X PHE 3.3 1.6 + - - +
15X HIS 3.0 0.2 - - - -
16X GLN* 1.3 90.6 - - + +
18X SER* 1.3 63.8 + - - +
19X GLY 3.4 2.4 + - - -
20X ARG* 3.5 48.7 + - - +
27X LEU* 3.6 18.8 - - + -
31X GLU* 3.1 28.7 - - - +
34X GLU* 3.7 12.6 - - + -
35X LEU* 3.6 39.5 - - + -
38X ASN* 3.3 16.6 - - - +
39X GLU* 2.5 44.7 + - + -
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Residues in contact with SER 18 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14X PHE* 2.8 39.8 + - - -
15X HIS* 3.5 18.9 + - - -
17X TYR* 1.3 73.6 - - - +
19X GLY* 1.3 58.6 + - - +
20X ARG 3.3 0.2 - - - -
21X GLU 3.6 0.2 - - - +
23X ASP 3.2 7.1 - - - +
24X LYS 2.7 22.5 + - - -
26X LYS 3.6 20.2 - - - -
27X LEU* 3.5 7.4 - - - +
31X GLU* 2.9 2.4 - - - +
103X CA 2.3 28.4 - - - -
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Residues in contact with GLY 19 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15X HIS* 3.5 11.8 + - - -
17X TYR 3.4 0.8 - - - -
18X SER* 1.3 79.9 + - - +
20X ARG* 1.3 63.0 + - - +
21X GLU 3.4 1.9 + - - +
24X LYS* 3.5 45.3 - - - +
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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