Contacts of the helix formed by residues 9 - 30 (chain B) in PDB entry 3CFV
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 9 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLU* 1.3 73.0 - - - +
10B THR* 1.3 59.9 + - - +
11B VAL* 3.1 23.0 + - - +
12B GLU* 3.4 34.8 + - + +
13B GLU* 2.9 29.5 + - - +
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Residues in contact with THR 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B MSE 4.5 20.2 - - + -
8B GLU* 3.6 19.2 + - + +
9B ASP* 1.3 73.4 + - - +
11B VAL* 1.3 68.3 + - - +
13B GLU* 3.8 15.6 - - - +
14B ARG* 2.8 41.7 + - - +
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Residues in contact with VAL 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ASP* 3.1 12.0 + - - +
10B THR* 1.3 82.2 + - - +
12B GLU* 1.3 66.1 + - - +
14B ARG* 3.3 21.1 + - - +
15B VAL* 3.5 18.6 + - + +
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Residues in contact with GLU 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ASP* 3.3 31.5 + - + +
11B VAL* 1.3 77.7 - - - +
13B GLU* 1.3 65.2 + - - +
15B VAL* 3.2 11.0 + - + +
16B ILE* 2.9 42.8 + - + +
339B ARG* 3.4 23.9 + - - +
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Residues in contact with GLU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLU* 3.0 40.1 - - + +
9B ASP 2.9 17.9 + - - +
10B THR* 3.8 15.2 - - - +
11B VAL 3.2 0.2 - - - -
12B GLU* 1.3 77.4 - - - +
14B ARG* 1.3 59.2 + - + +
16B ILE* 3.4 10.1 + - - +
17B ASN* 2.9 47.6 + - - +
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Residues in contact with ARG 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B THR* 2.8 39.0 + - - +
11B VAL* 3.3 15.4 + - - +
12B GLU 3.3 0.2 - - - -
13B GLU* 1.3 79.4 - - + +
15B VAL* 1.3 64.1 + - + +
17B ASN* 3.4 6.4 + - - +
18B GLU* 3.0 32.1 + - + +
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Residues in contact with VAL 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B VAL* 3.5 17.5 + - + +
12B GLU* 3.2 12.5 + - + +
14B ARG* 1.3 78.5 - - + +
16B ILE* 1.3 65.4 + - + +
18B GLU* 3.3 5.1 + - - +
19B GLU* 3.1 44.4 + - + +
339B ARG* 5.9 2.9 - - - +
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Residues in contact with ILE 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLU* 2.9 38.3 + - + +
13B GLU* 3.7 7.4 - - + +
15B VAL* 1.3 77.5 - - + +
17B ASN* 1.3 60.4 + - - +
19B GLU* 3.4 6.8 + - - +
20B TYR* 3.0 25.6 + - - +
339B ARG* 3.7 44.4 - - - +
372B HIS 5.2 0.7 - - - +
373B THR* 3.5 47.6 - - + +
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Residues in contact with ASN 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLU* 2.9 39.2 + - - +
14B ARG* 3.7 6.6 - - - +
16B ILE* 1.3 85.3 - - - +
18B GLU* 1.3 59.8 + - + +
20B TYR* 3.1 9.4 + - - +
21B LYS* 2.9 39.2 + - - +
373B THR* 4.6 8.7 - - - +
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Residues in contact with GLU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ARG* 3.0 22.6 + - + +
15B VAL* 3.9 5.2 - - - +
17B ASN* 1.3 76.9 - - + +
19B GLU* 1.3 62.0 + - + +
21B LYS* 3.0 39.7 + - - +
22B ILE* 3.3 31.5 + - + +
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Residues in contact with GLU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B VAL* 3.1 36.7 + - + +
16B ILE* 3.7 7.1 - - - +
18B GLU* 1.3 76.4 - - + +
20B TYR* 1.3 59.0 + - - +
22B ILE* 3.7 9.1 + - + +
23B TRP* 3.1 25.8 + - - +
339B ARG* 4.9 5.3 + - - -
340B ARG* 2.8 31.6 + - - +
370B GLY 5.3 0.4 - - - +
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Residues in contact with TYR 20 (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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16B ILE 3.0 14.6 + - - +
17B ASN* 3.1 12.3 + - - +
19B GLU* 1.3 75.8 - - - +
21B LYS* 1.3 71.7 + - + +
23B TRP* 3.1 30.9 + + - +
24B LYS* 2.9 49.8 + - + +
36B THR* 5.2 7.4 + - - +
370B GLY 4.7 3.8 - - - -
371B GLY 3.3 25.1 - - - -
372B HIS 5.3 0.4 - - - -
373B THR* 3.6 28.5 - - + -
399B GLN* 4.9 3.3 + - - -
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Residues in contact with LYS 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ASN* 2.9 21.9 + - - +
18B GLU* 3.0 42.7 + - - +
20B TYR* 1.3 82.1 - - + +
22B ILE* 1.3 63.3 + - + +
24B LYS* 3.3 15.2 + - - +
25B LYS* 3.1 30.0 + - - +
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Residues in contact with ILE 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLU* 3.3 20.3 + - + +
19B GLU* 3.9 9.0 - - + +
20B TYR 3.2 0.4 - - - -
21B LYS* 1.3 75.0 - - + +
23B TRP* 1.3 65.8 + - - +
25B LYS* 3.3 28.6 - - + +
26B ASN* 3.4 23.1 + - - +
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Residues in contact with TRP 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLU 3.1 15.9 + - - +
20B TYR* 3.1 41.5 + + - +
22B ILE* 1.3 78.1 - - - +
24B LYS* 1.3 81.9 + - + +
26B ASN* 3.1 17.9 + - - +
27B THR* 3.2 26.3 + - + +
30B LEU* 5.1 3.3 - - + +
31B TYR* 2.7 47.7 + + - -
34B VAL* 4.4 11.2 - - + -
36B THR* 5.6 2.5 - - + -
369B HIS* 4.0 5.2 - + - -
370B GLY* 3.2 27.4 - - - +
371B GLY* 3.4 19.5 - - - -
399B GLN* 4.1 10.3 - - - -
41E GLY 3.4 28.3 - - - +
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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
----------------------------------------------------------
20B TYR* 2.9 41.4 + - + +
21B LYS* 3.5 8.7 - - - +
22B ILE 3.2 0.4 - - - -
23B TRP* 1.3 93.5 - - + +
25B LYS* 1.3 59.1 + - - +
26B ASN 3.1 0.2 - - - -
27B THR* 2.6 29.2 + - + +
28B PRO* 3.9 1.2 - - - +
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Residues in contact with LYS 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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21B LYS* 3.1 29.1 + - - +
22B ILE* 3.3 25.6 - - + +
24B LYS* 1.3 79.0 - - - +
26B ASN* 1.3 65.9 + - - +
27B THR 3.4 0.2 - - - -
28B PRO* 3.5 14.1 - - - +
29B PHE* 4.4 8.1 - - - -
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Residues in contact with ASN 26 (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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22B ILE* 3.4 26.4 + - - +
23B TRP* 3.4 12.4 - - - +
24B LYS 3.1 0.8 - - - -
25B LYS* 1.3 85.0 + - - +
27B THR* 1.3 62.7 + - - +
28B PRO* 3.2 3.8 - - - -
29B PHE* 3.0 33.2 + - - +
30B LEU* 3.3 20.7 + - + +
37E LEU* 3.6 32.3 - - + +
41E GLY 5.5 3.8 - - - +
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Residues in contact with THR 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TRP* 3.2 52.9 + - + +
24B LYS* 2.6 21.6 + - + +
26B ASN* 1.3 76.7 - - - +
28B PRO* 1.3 68.7 - - - +
30B LEU 2.9 0.7 + - - -
31B TYR* 2.8 51.1 + - + +
34B VAL* 4.3 16.2 - - + +
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Residues in contact with PRO 28 (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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24B LYS 3.9 0.7 - - - +
25B LYS* 3.5 15.3 - - - +
26B ASN 3.2 5.4 - - - -
27B THR* 1.3 100.6 - - - +
29B PHE* 1.3 66.0 + - + +
31B TYR 4.1 9.7 - - - +
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Residues in contact with PHE 29 (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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25B LYS 4.4 7.2 - - - -
26B ASN* 3.0 34.3 + - - +
28B PRO* 1.3 84.1 - - + +
30B LEU* 1.3 62.6 + - + +
31B TYR 3.6 0.4 - - - -
404B ALA* 3.8 10.7 - - - +
406B ASN* 5.5 0.9 + - - -
34E ILE* 3.6 44.1 - - + +
37E LEU* 4.0 13.2 - - + -
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Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TRP* 5.1 4.0 - - + +
26B ASN* 3.3 18.6 + - + +
27B THR 2.9 1.6 + - - -
29B PHE* 1.3 79.0 - - - +
31B TYR* 1.3 82.5 + - + +
367B PHE* 3.7 20.1 - - + -
368B ILE 5.5 0.9 - - - +
403B MSE 3.7 0.9 - - - -
404B ALA* 2.9 22.6 + - - +
407B ILE* 3.9 6.8 - - + +
34E ILE* 3.8 11.7 - - + +
37E LEU* 4.0 33.0 - - + +
38E ALA* 3.6 37.0 - - + +
41E GLY 4.0 17.9 - - - +
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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
------------------------------------------------------------
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