Contacts of the helix formed by residues 13 - 26 (chain B) in PDB entry 1V2E
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 13 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A GLN* 2.5 33.6 + - - +
250A TRP* 4.1 6.5 - - - -
253A PHE* 4.0 8.7 - - - -
11B LYS 4.1 1.8 - - - -
12B GLU* 1.3 89.7 - - - +
14B ILE* 1.3 68.3 + - - +
15B PHE* 4.6 1.3 - - - -
16B PRO* 2.9 32.3 - - - +
17B ARG* 3.5 2.1 - - - +
113B ASP* 4.0 24.2 - - - -
1520B KMT 5.5 0.2 - - - -
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Residues in contact with ILE 14 (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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12B GLU 3.8 1.6 + - - -
13B SER* 1.3 70.9 - - - +
15B PHE* 1.3 93.5 + - + +
17B ARG* 2.8 18.5 + - - +
18B MET* 2.8 45.2 + - + +
113B ASP* 4.9 3.1 - - + +
320B PHE* 4.4 27.1 - - + -
331B ILE* 4.6 9.9 - - + -
332B PRO* 5.3 11.2 - - + -
335B ALA* 4.0 22.9 - - + -
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Residues in contact with PHE 15 (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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13B SER* 5.0 0.4 - - - -
14B ILE* 1.3 96.9 - - + +
16B PRO* 1.3 68.1 - - + +
18B MET* 4.1 5.2 - - - +
19B SER* 3.2 26.9 + - - -
32B GLN* 3.2 24.1 - - + +
112B PHE* 5.5 2.9 - + - -
113B ASP* 2.7 37.2 - - + -
331B ILE* 3.8 24.7 - - + -
335B ALA* 5.0 2.0 - - + -
336B PHE* 4.0 17.3 - + - -
347B ARG* 3.0 43.7 - - - -
1520B KMT 3.9 29.4 - - + -
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Residues in contact with PRO 16 (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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59A PRO* 4.9 7.6 - - + +
60A PRO* 3.4 35.9 - - + -
249A GLN* 4.6 0.2 - - - +
253A PHE* 4.3 12.1 - - + -
12B GLU* 4.6 8.7 - - + +
13B SER* 2.9 36.8 - - - +
15B PHE* 1.3 94.3 - - + +
17B ARG* 1.3 61.0 + - - +
19B SER* 3.8 2.9 - - - -
20B GLY* 3.2 18.4 + - - -
32B GLN* 3.8 11.7 - - - +
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Residues in contact with ARG 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLU* 3.2 39.1 + - - +
13B SER 3.5 5.2 - - - +
14B ILE* 2.8 18.3 + - + +
16B PRO* 1.3 82.1 - - - +
18B MET* 1.3 60.3 + - - +
20B GLY* 3.6 1.8 + - - -
21B LEU* 3.3 20.8 + - - +
320B PHE* 3.4 37.5 - - + -
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Residues in contact with MET 18 (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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14B ILE* 2.8 27.2 + - + +
15B PHE 4.2 3.4 - - - +
17B ARG* 1.3 75.4 - - - +
19B SER* 1.3 61.3 + - - +
20B GLY 3.2 0.4 - - - -
21B LEU* 3.7 26.7 - - + -
22B ALA* 2.8 30.8 + - - +
29B ASN* 4.8 2.5 - - - +
31B GLY* 6.1 0.2 - - - -
32B GLN 6.0 1.3 - - - +
319B ALA* 5.3 8.1 - - + +
320B PHE* 5.2 13.0 - - + -
323B VAL* 4.2 15.9 - - + -
329B ALA* 3.3 42.2 - - + -
330B LEU 3.4 22.9 - - - +
331B ILE* 4.6 14.4 - - + -
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Residues in contact with SER 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE 3.2 8.7 + - - -
16B PRO* 3.8 4.9 - - - -
17B ARG 3.3 0.2 - - - -
18B MET* 1.3 77.7 - - - +
20B GLY* 1.3 59.4 + - - +
22B ALA* 3.9 0.3 - - - +
23B GLN* 3.0 31.2 + - - +
29B ASN* 2.6 31.2 + - - +
32B GLN* 2.6 37.4 + - - +
34B PHE* 4.1 4.1 - - - -
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Residues in contact with GLY 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B PRO 3.2 12.7 + - - -
17B ARG* 3.6 2.9 + - - -
18B MET 3.2 0.2 - - - -
19B SER* 1.3 79.8 - - - +
21B LEU* 1.3 55.8 + - - +
23B GLN* 3.9 8.8 + - - +
24B ARG* 3.0 33.6 + - - +
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Residues in contact with LEU 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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17B ARG 3.3 16.2 + - - +
18B MET* 3.7 13.0 - - + +
19B SER 3.3 0.2 - - - -
20B GLY* 1.3 74.7 - - - +
22B ALA* 1.3 65.9 + - - +
24B ARG* 3.9 24.7 - - - +
25B LEU* 2.9 53.8 + - + +
320B PHE* 3.2 40.2 - - + -
323B VAL* 3.5 20.0 - - + -
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Residues in contact with ALA 22 (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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18B MET 2.8 21.9 + - - +
19B SER 3.9 3.6 - - - +
21B LEU* 1.3 73.5 - - - +
23B GLN* 1.3 63.6 + - - +
25B LEU 3.1 2.4 + - - -
26B GLY 3.0 4.3 + - - -
27B ALA* 2.9 37.4 + - + +
29B ASN* 4.0 12.1 - - + -
323B VAL* 3.8 14.3 - - + +
329B ALA* 3.7 26.2 - - + -
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Residues in contact with GLN 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 SER 3.0 20.8 + - - +
20B GLY* 3.9 8.7 + - - +
22B ALA* 1.3 76.8 - - - +
24B ARG* 1.3 70.9 + - - +
26B GLY* 2.9 15.6 + - - -
27B ALA 4.9 2.5 - - - +
29B ASN* 5.3 1.0 - - - +
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Residues in contact with ARG 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B GLY 3.0 19.0 + - - +
21B LEU* 3.8 27.6 - - - +
23B GLN* 1.3 85.8 - - + +
25B LEU* 1.3 72.1 + - - +
26B GLY 3.7 0.3 + - - -
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Residues in contact with LEU 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 LEU* 2.9 53.9 + - + +
22B ALA 3.7 3.1 - - - +
23B GLN 3.1 0.2 - - - -
24B ARG* 1.3 91.6 - - - +
26B GLY* 1.3 62.0 + - - +
27B ALA 4.4 0.7 - - - +
323B VAL* 3.1 32.1 - - + +
324B GLU* 4.7 11.4 - - + +
327B ARG* 2.9 55.4 + - - +
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Residues in contact with GLY 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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23B GLN* 2.9 14.6 + - - -
24B ARG 3.4 1.2 + - - -
25B LEU* 1.3 80.0 - - - +
27B ALA* 1.3 58.1 + - - +
327B ARG* 4.6 2.7 + - - +
363B ARG* 3.2 19.9 + - - -
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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
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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