Contacts of the helix formed by residues 39 - 54 (chain A) in PDB entry 3D9L
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 PHE 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A ALA* 4.5 18.2 - - + -
4A VAL* 3.6 28.3 - - + -
36A ALA* 2.8 14.6 + - - +
38A LYS* 1.3 121.6 - - + +
40A TYR* 1.3 56.4 + - - +
41A LYS* 3.1 4.0 - - - -
42A HIS* 2.9 40.5 + + - +
43A VAL* 3.1 10.7 + - - +
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Residues in contact with TYR 40 (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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36A ALA 3.5 2.9 + - - -
37A ILE 3.3 19.6 + - - +
38A LYS 4.3 6.5 - - - -
39A PHE* 1.3 76.1 - - - +
41A LYS* 1.3 88.3 + - + +
43A VAL* 3.5 3.5 - - - +
44A VAL* 2.9 34.2 + - + +
83A VAL* 3.7 50.4 - - + +
84A PHE* 3.7 25.8 - + + -
87A ARG* 3.9 19.3 - - + -
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Residues in contact with LYS 41 (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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39A PHE 3.0 1.0 + - - -
40A TYR* 1.3 110.9 - - + +
42A HIS* 1.3 65.3 + - + +
44A VAL* 3.7 2.3 + - - +
45A GLN* 3.0 26.9 + - - +
87A ARG* 3.6 52.0 + - - +
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Residues in contact with HIS 42 (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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4A VAL* 4.0 28.9 - - + -
39A PHE* 2.9 29.8 + + - +
41A LYS* 1.3 82.2 - - + +
43A VAL* 1.3 58.8 - - - +
45A GLN* 3.3 20.0 + - - +
46A SER* 2.8 34.5 + - - -
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Residues in contact with VAL 43 (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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4A VAL* 5.3 5.6 - - + +
7A PHE* 3.7 37.0 - - + -
33A ALA* 3.8 17.7 - - + +
36A ALA* 3.9 31.4 - - + +
39A PHE 3.1 12.5 + - - +
40A TYR* 3.5 8.1 - - - +
42A HIS* 1.3 72.8 - - - +
44A VAL* 1.3 65.8 + - - +
46A SER* 3.3 2.6 + - - -
47A VAL* 3.0 24.9 + - + +
69A ILE* 4.2 6.5 - - + -
84A PHE* 3.7 20.0 - - + -
88A PHE* 5.4 0.7 - - + -
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Residues in contact with VAL 44 (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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40A TYR 2.9 21.3 + - - +
41A LYS 4.0 2.9 - - - +
43A VAL* 1.3 74.8 - - - +
45A GLN* 1.3 64.2 + - - +
47A VAL* 3.3 2.4 + - - +
48A GLU* 2.9 48.4 + - - +
84A PHE* 4.1 10.8 - - + -
87A ARG* 3.5 42.8 - - + +
88A PHE* 3.7 39.5 - - + -
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Residues in contact with GLN 45 (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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41A LYS 3.0 19.4 + - - +
42A HIS* 3.5 22.8 - - - +
43A VAL 3.3 0.2 - - - -
44A VAL* 1.3 76.9 - - - +
46A SER* 1.3 57.4 + - - +
48A GLU* 3.7 10.3 - - - +
49A LYS* 2.8 31.5 + - + +
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Residues in contact with SER 46 (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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4A VAL* 4.7 3.5 - - - +
7A PHE* 4.1 10.5 - - - -
8A ASN* 2.8 32.8 + - - -
11A LEU* 3.5 6.7 - - - +
12A TYR* 3.8 6.2 + - - -
42A HIS* 2.8 23.3 + - - +
43A VAL* 3.7 4.7 - - - -
45A GLN* 1.3 71.3 + - - +
47A VAL* 1.3 58.1 + - - +
49A LYS* 3.4 7.6 + - - +
50A PHE* 2.9 30.3 + - - +
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Residues in contact with VAL 47 (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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7A PHE* 3.5 25.8 - - + -
11A LEU* 3.9 9.2 - - + -
43A VAL 3.0 20.3 + - - +
44A VAL 3.7 3.8 - - - +
46A SER* 1.3 77.0 - - - +
48A GLU* 1.3 56.5 + - - +
50A PHE* 3.4 3.2 + - + +
51A ILE* 3.0 37.2 + - + +
62A GLY* 4.2 2.0 - - - +
65A VAL* 3.7 22.4 - - + -
66A ILE* 3.7 31.0 - - + -
69A ILE* 4.2 2.5 - - + -
88A PHE* 3.8 16.2 - - + -
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Residues in contact with GLU 48 (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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44A VAL* 2.9 39.6 + - + +
45A GLN* 3.7 8.7 - - - +
47A VAL* 1.3 72.3 - - + +
49A LYS* 1.3 61.4 + - - +
51A ILE* 3.4 9.2 + - - +
52A GLN* 2.9 29.2 + - - +
87A ARG 4.5 1.2 - - - +
88A PHE* 4.1 20.7 - - + +
91A ASN* 3.1 42.8 + - - +
95A THR* 3.8 19.9 + - + +
98A ASN* 5.0 1.7 + - - -
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Residues in contact with LYS 49 (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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12A TYR* 3.5 18.4 - - - +
45A GLN* 2.8 23.9 + - + +
46A SER* 3.7 8.1 - - - +
48A GLU* 1.3 72.0 - - - +
50A PHE* 1.3 61.2 + - - +
52A GLN* 3.0 12.7 + - - +
53A LYS* 3.0 52.2 + - + +
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Residues in contact with PHE 50 (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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11A LEU* 3.8 34.8 - - + -
12A TYR* 3.4 31.0 + + - +
14A LEU* 3.7 28.9 - - + -
15A ASN* 3.8 22.2 - - - -
46A SER 2.9 17.9 + - - +
47A VAL* 3.5 4.9 - - + +
49A LYS* 1.3 75.0 - - - +
51A ILE* 1.3 62.6 + - + +
53A LYS* 5.0 1.6 - - - -
54A CYS* 2.8 50.1 + - + +
58A TYR* 3.8 39.0 - + + -
62A GLY* 4.1 12.1 - - - -
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Residues in contact with ILE 51 (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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47A VAL* 3.0 25.5 + - + +
48A GLU* 3.7 6.3 - - - +
50A PHE* 1.3 76.7 - - + +
52A GLN* 1.3 57.2 + - - +
54A CYS* 4.1 6.7 - - - -
59A LYS* 2.8 27.6 + - + +
62A GLY* 3.7 34.5 - - - +
66A ILE* 3.7 30.5 - - + -
95A THR* 3.7 33.2 - - + +
98A ASN* 3.7 11.7 - - + +
99A LEU* 3.7 20.9 - - + +
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Residues in contact with GLN 52 (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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48A GLU 2.9 14.2 + - - +
49A LYS* 3.0 15.5 + - - +
51A ILE* 1.3 78.9 - - - +
53A LYS* 1.3 85.6 + - + +
59A LYS* 3.8 6.2 + - - -
98A ASN* 3.8 26.9 - - - +
101A ARG* 4.4 14.3 + - - +
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Residues in contact with LYS 53 (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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12A TYR* 5.6 5.2 - - + +
49A LYS* 3.0 40.6 + - + +
50A PHE* 4.3 2.2 - - - +
52A GLN* 1.3 104.7 - - + +
54A CYS* 1.3 70.3 + - - +
55A LYS 3.7 0.2 + - - -
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Residues in contact with CYS 54 (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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15A ASN* 5.4 2.7 - - - +
50A PHE* 2.8 44.5 + - + +
51A ILE* 4.0 4.5 - - - -
52A GLN 3.7 0.2 - - - -
53A LYS* 1.3 77.0 - - - +
55A LYS* 1.3 70.9 + - - +
56A PRO* 3.9 1.2 - - - +
58A TYR* 3.7 31.4 - - + -
59A LYS* 2.8 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