Contacts of the helix formed by residues 21 - 33 (chain A) in PDB entry 4CQM
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 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A GLY 3.4 9.3 + - - +
19A ALA 3.2 2.2 + - - -
20A GLY* 1.3 82.7 - - - +
22A GLY* 1.3 75.3 + - - +
23A ILE 3.3 0.7 + - - -
24A GLY 3.3 13.0 + - - -
25A ARG* 3.4 10.9 + - - +
42A ASP* 4.3 1.7 + - - -
47A ALA* 5.7 1.1 - - - -
205A PRO* 3.2 26.5 - - - +
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Residues in contact with GLY 22 (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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21A SER* 1.3 78.3 + - - +
23A ILE* 1.3 62.4 + - - -
25A ARG* 3.5 5.6 + - - +
26A ALA* 3.3 21.1 + - - +
204A THR* 3.8 21.1 - - - -
205A PRO* 3.9 13.1 - - - +
230A PRO* 4.0 6.5 - - - +
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Residues in contact with ILE 23 (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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21A SER 3.3 1.0 + - - -
22A GLY* 1.3 70.3 - - - -
24A GLY* 1.3 61.9 + - - +
26A ALA* 3.2 3.2 + - - +
27A VAL* 2.8 44.6 + - + +
103A CYS* 4.1 14.1 - - + +
154A ILE* 4.5 13.0 - - + -
199A PRO* 4.5 13.7 - - + -
202A ILE* 4.6 7.4 - - + -
204A THR* 3.8 19.4 - - + +
230A PRO* 4.4 8.7 - - + +
233A VAL* 3.7 45.3 - - + -
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Residues in contact with GLY 24 (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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16A VAL* 3.5 7.5 - - - +
18A GLY 3.4 16.8 + - - -
19A ALA* 3.5 10.3 - - - -
21A SER 3.3 4.4 + - - -
23A ILE* 1.3 79.1 - - - +
25A ARG* 1.3 58.8 + - - +
27A VAL* 3.6 0.6 + - - +
28A SER* 2.9 27.4 + - - -
103A CYS* 3.7 24.7 - - - +
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Residues in contact with ARG 25 (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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19A ALA 3.3 13.7 + - - +
20A GLY 2.9 22.9 + - - -
21A SER* 3.4 16.2 + - - +
22A GLY 3.9 8.5 - - - +
23A ILE 3.2 0.4 - - - -
24A GLY* 1.3 72.6 - - - +
26A ALA* 1.3 62.4 + - - +
28A SER* 3.2 4.3 + - - -
29A VAL* 3.0 36.3 + - + +
47A ALA 3.3 15.4 + - - -
50A GLU* 3.0 36.5 + - - +
51A THR* 3.0 23.7 + - + +
54A LEU* 3.8 29.5 - - + +
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Residues in contact with ALA 26 (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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22A GLY 3.3 4.2 + - - +
23A ILE 3.2 6.4 + - - +
25A ARG* 1.3 77.6 - - - +
27A VAL* 1.3 59.7 + - - +
29A VAL* 3.3 9.3 + - - +
30A ARG* 2.9 30.7 + - - +
230A PRO* 3.5 43.5 - - + +
231A GLU* 4.3 11.8 - - + +
234A ALA* 3.7 4.2 - - + +
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Residues in contact with VAL 27 (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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16A VAL* 3.7 16.2 - - + -
23A ILE* 2.8 36.1 + - + +
24A GLY* 3.7 6.7 - - - +
26A ALA* 1.3 76.9 - - - +
28A SER* 1.3 54.0 + - - +
30A ARG* 3.2 1.4 + - - +
31A LEU* 2.8 63.3 + - + +
101A VAL* 4.5 2.9 - - + -
103A CYS* 4.1 7.2 - - - -
234A ALA* 3.8 15.7 - - + -
237A VAL* 3.9 32.1 - - + -
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Residues in contact with SER 28 (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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16A VAL* 4.0 4.1 - - - +
19A ALA* 3.4 18.2 - - - +
24A GLY 2.9 13.8 + - - -
25A ARG 3.4 8.5 - - - -
27A VAL* 1.3 79.5 - - - +
29A VAL* 1.3 57.8 + - - +
31A LEU* 4.6 0.9 - - - -
32A ALA* 3.0 32.9 + - - +
38A VAL* 3.5 30.3 - - - +
51A THR* 3.8 17.9 - - - +
55A LEU* 3.3 6.9 - - - +
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Residues in contact with VAL 29 (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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25A ARG* 3.0 29.8 + - + +
26A ALA* 3.5 10.5 - - - +
27A VAL 3.2 0.2 - - - -
28A SER* 1.3 77.5 - - - +
30A ARG* 1.3 58.2 + - - +
32A ALA* 3.8 1.0 - - - +
33A GLY* 2.8 26.7 + - - -
51A THR* 5.5 0.4 - - + -
54A LEU* 5.1 14.4 - - + +
55A LEU* 3.7 15.9 - - + -
231A GLU* 6.0 2.5 - - - +
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Residues in contact with ARG 30 (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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6A GLN* 6.0 0.2 + - - -
8A ARG* 3.8 16.0 - - - +
26A ALA 2.9 16.4 + - - +
27A VAL 3.7 2.9 - - - +
29A VAL* 1.3 76.4 - - - +
31A LEU* 1.3 66.4 + - + +
33A GLY* 3.2 3.4 + - - -
34A GLU* 2.6 52.5 + - - +
231A GLU* 4.7 5.2 + - + +
234A ALA* 3.9 17.3 - - + +
235A ASP* 3.1 43.9 + - - +
238A ALA* 3.8 20.6 - - + +
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Residues in contact with LEU 31 (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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9A LEU* 3.6 25.4 - - + -
14A ALA* 3.6 24.5 - - + -
16A VAL* 4.0 10.3 - - + -
27A VAL* 2.8 43.9 + - + +
30A ARG* 1.3 73.3 - - + +
32A ALA* 1.3 58.3 + - - +
34A GLU* 3.0 18.0 + - - +
36A ALA* 3.2 27.1 + - + +
38A VAL* 4.1 10.5 - - + -
99A VAL* 4.3 13.2 - - + -
101A VAL* 4.6 2.0 - - + -
234A ALA 5.4 0.2 - - - +
237A VAL* 4.5 9.6 - - + -
238A ALA* 4.1 19.5 - - + +
241A ALA* 4.7 4.5 - - + -
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Residues in contact with ALA 32 (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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28A SER 3.0 20.4 + - - +
29A VAL 4.0 1.1 - - - +
31A LEU* 1.3 76.0 - - - +
33A GLY* 1.3 61.1 + - - +
34A GLU 3.0 1.3 + - - -
35A GLY* 3.2 12.8 + - - -
36A ALA 3.3 12.7 - - - +
38A VAL* 3.7 5.1 - - + +
55A LEU* 3.8 17.0 - - + -
65A PRO* 5.2 9.4 - - - +
66A ARG 5.4 2.6 - - - +
69A HIS* 3.7 28.3 + - + +
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Residues in contact with GLY 33 (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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6A GLN* 3.5 20.8 + - - +
29A VAL 2.8 19.0 + - - -
30A ARG* 3.2 5.4 + - - -
31A LEU 3.2 0.6 - - - -
32A ALA* 1.3 76.0 - - - +
34A GLU* 1.3 58.8 + - - +
35A GLY 3.4 1.5 + - - -
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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