Contacts of the helix formed by residues 35 - 49 (chain D) in PDB entry 2P5V
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 35 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29D SER* 3.8 1.3 - - - -
34D LEU* 1.3 74.8 - - - +
36D PRO* 1.3 76.2 - - - +
37D SER* 3.2 1.7 + - - -
38D PRO* 3.2 22.5 - - - +
39D CYS* 3.0 23.0 + - - +
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Residues in contact with PRO 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D ASN* 2.8 31.1 - - - +
26D VAL* 4.5 21.1 - - + -
29D SER* 3.7 21.1 - - - +
35D SER* 1.3 88.1 - - - +
37D SER* 1.3 56.5 + - - +
39D CYS* 4.1 0.4 - - + -
40D LEU* 2.8 22.5 + - - +
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Residues in contact with SER 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D SER* 4.5 0.9 - - - -
36D PRO* 1.3 76.8 - - - +
38D PRO* 1.4 76.8 - - - +
40D LEU* 3.3 7.9 + - - +
41D ARG* 3.1 23.1 + - - +
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Residues in contact with PRO 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D LEU* 4.8 12.6 - - + -
35D SER* 3.2 30.5 - - - +
37D SER* 1.4 98.1 - - - +
39D CYS* 1.3 54.9 + - - +
41D ARG* 3.4 8.8 + - + +
42D ARG* 3.0 36.2 + - + +
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Residues in contact with CYS 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ILE* 4.4 4.2 - - - +
25D ASN* 3.9 7.6 - - - +
28D LEU* 3.8 20.2 - - - -
29D SER* 3.5 32.8 - - - -
32D VAL* 3.8 12.1 - - - -
34D LEU* 3.9 17.5 - - + +
35D SER 3.0 21.7 + - - +
36D PRO 3.6 4.7 - - - +
38D PRO* 1.3 75.1 - - - +
40D LEU* 1.3 59.1 + - - +
42D ARG* 3.4 4.1 + - - +
43D LEU* 3.0 26.5 + - - +
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Residues in contact with LEU 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D ASN* 3.6 26.9 - - + +
36D PRO 2.8 18.4 + - - +
37D SER* 3.7 7.6 - - - +
39D CYS* 1.3 73.1 - - - +
41D ARG* 1.3 60.3 + - - +
43D LEU* 3.2 15.0 + - + +
44D LYS* 3.0 28.2 + - - +
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Residues in contact with ARG 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D SER 3.1 16.7 + - - +
38D PRO* 3.5 9.4 - - + +
40D LEU* 1.3 77.3 - - - +
42D ARG* 1.3 64.7 + - + +
44D LYS* 3.5 35.1 + - - +
45D GLN* 2.8 40.4 + - - +
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Residues in contact with ARG 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D ASP* 3.0 28.0 + - - -
9D THR* 3.3 25.4 + - - -
10D ASP* 3.1 35.8 + - - +
13D ILE* 3.4 22.7 - - + +
34D LEU* 4.4 15.8 - - + +
38D PRO* 3.0 23.3 + - + +
39D CYS 3.5 4.0 - - - +
41D ARG* 1.3 77.2 - - + +
43D LEU* 1.3 62.0 + - - +
45D GLN* 2.9 38.7 - - - +
46D LEU* 3.3 14.0 + - - +
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Residues in contact with LEU 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ARG* 6.0 5.6 - - - +
13D ILE* 4.4 7.3 - - + +
17D LEU* 3.3 37.0 - - + -
25D ASN* 4.8 10.1 - - + +
28D LEU* 3.9 20.4 - - + -
39D CYS 3.0 14.5 + - - +
40D LEU* 3.2 17.9 + - + +
42D ARG* 1.3 73.4 - - - +
44D LYS* 1.3 69.0 + - - +
46D LEU* 3.4 10.0 + - + +
47D GLU* 3.0 44.9 + - + +
52D VAL* 5.7 1.3 - - + -
55D TYR* 4.5 2.7 - - - +
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Residues in contact with LYS 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D LEU 3.0 12.0 + - - +
41D ARG* 3.5 29.3 - - - +
43D LEU* 1.3 72.9 - - - +
45D GLN* 1.3 52.7 + - - +
47D GLU* 2.9 11.1 + - - +
48D ASP* 2.7 64.8 + - - +
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Residues in contact with GLN 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ASP* 4.2 9.5 + - - -
41D ARG* 2.8 42.4 + - - +
42D ARG* 2.9 50.5 + - - +
44D LYS* 1.3 79.1 - - - +
46D LEU* 1.3 59.5 + - + +
48D ASP* 3.6 8.2 - - - +
49D ALA* 2.9 29.5 + - - +
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Residues in contact with LEU 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D LEU* 4.2 21.3 - - + -
10D ASP* 3.9 33.0 - - + +
13D ILE* 3.7 30.7 - - + -
14D LEU* 4.2 18.2 - - + -
42D ARG 3.3 16.7 + - - +
43D LEU* 3.7 9.2 - - + +
44D LYS 3.2 0.6 - - - -
45D GLN* 1.3 79.2 - - + +
47D GLU* 1.3 62.4 + - - +
49D ALA* 3.3 9.1 + - - +
51D ILE* 3.4 47.5 + - + +
52D VAL* 4.1 3.1 + - + -
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Residues in contact with GLU 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ARG* 5.4 1.2 - - - -
43D LEU* 3.0 32.1 + - - +
44D LYS* 2.9 11.4 + - + +
46D LEU* 1.3 77.1 - - - +
48D ASP* 1.3 65.5 + - - +
49D ALA 3.5 0.9 + - - -
50D GLY* 3.5 11.8 + - - -
52D VAL* 4.5 23.7 - - + +
55D TYR* 2.4 41.4 + - + +
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Residues in contact with ASP 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D LYS* 2.7 61.4 + - - +
45D GLN* 3.6 8.7 - - - +
47D GLU* 1.3 79.1 - - - +
49D ALA* 1.3 57.9 + - - +
50D GLY 3.3 0.4 - - - -
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Residues in contact with ALA 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C SER* 5.0 4.2 - - - -
4D LEU* 6.4 1.3 - - + -
45D GLN 2.9 17.3 + - - +
46D LEU* 3.6 6.7 - - - +
47D GLU 3.2 1.0 - - - -
48D ASP* 1.3 77.1 - - - +
50D GLY* 1.3 59.9 + - - +
51D ILE* 3.3 19.8 + - + +
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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