Contacts of the helix formed by residues 40 - 49 (chain V) in PDB entry 3DLL
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 PRO 40 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37V LEU* 5.2 2.0 - - + +
38V ALA* 2.5 26.0 - - - +
39V GLN* 1.3 74.1 - - - +
41V HIS* 1.3 58.4 + - - +
43V VAL* 3.0 25.9 - - + +
44V ARG* 4.1 9.2 + - - +
60X A 4.4 21.6 + - + +
93X A 4.1 21.1 - - + +
94X C 2.7 48.7 - - - +
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Residues in contact with HIS 41 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39V GLN* 4.4 12.1 - - + -
40V PRO* 1.3 74.7 - - + +
42V ARG* 1.3 61.9 + - + +
43V VAL 2.5 16.8 + - - -
44V ARG* 3.1 17.0 + - - +
45V GLN* 2.7 42.1 + - + +
94X C 2.7 38.7 + - - +
95X G 3.3 55.5 + - - +
96X C 5.0 4.0 - - - -
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Residues in contact with ARG 42 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21V ARG* 4.7 12.1 - - - +
24V GLU* 3.9 11.0 + - - +
28V LEU* 5.1 8.6 - - + +
39V GLN* 3.6 41.5 - - + +
41V HIS* 1.3 85.6 - - + +
43V VAL* 1.3 57.2 + - - +
45V GLN* 2.7 51.8 + - - +
46V LEU* 3.0 52.8 - - + +
49V GLU* 4.5 6.5 + - - -
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Residues in contact with VAL 43 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25V LEU* 3.8 10.2 - - + +
28V LEU* 4.6 10.3 - - + -
37V LEU* 4.5 14.8 - - + -
39V GLN 3.1 17.7 - - - +
40V PRO* 3.0 21.5 - - + +
41V HIS 2.5 5.5 + - - -
42V ARG* 1.3 73.4 - - - +
44V ARG* 1.3 68.2 + - - +
45V GLN 3.0 1.3 + - - -
46V LEU 3.3 3.1 + - - -
47V ARG* 3.1 29.3 + - + +
59X G 6.0 0.9 - - - +
60X A 3.3 32.5 - - - +
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Residues in contact with ARG 44 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40V PRO 4.3 6.1 + - - +
41V HIS* 3.1 15.0 + - - +
43V VAL* 1.3 80.2 - - - +
45V GLN* 1.3 65.9 - - - +
47V ARG* 3.0 23.0 + - - +
48V ARG* 3.2 10.0 + - - +
59X G 4.8 6.1 - - - +
60X A 3.5 28.9 - - - +
73X A 5.8 0.8 + - - -
74X G 5.4 5.5 + - - -
86X U 4.2 17.9 + - - -
94X C 5.2 6.7 + - - -
95X G 4.1 24.9 + - - +
96X C 5.6 2.4 + - - -
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Residues in contact with GLN 45 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41V HIS* 2.7 29.4 + - + +
42V ARG* 2.7 65.9 + - - +
43V VAL 3.0 0.6 - - - -
44V ARG* 1.3 77.5 - - - +
46V LEU* 1.3 68.7 + - - +
48V ARG* 3.0 11.7 + - - +
49V GLU* 2.9 31.4 + - + +
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Residues in contact with LEU 46 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21V ARG* 4.7 13.7 - - + -
24V GLU* 2.7 45.3 - - + +
25V LEU* 4.0 23.3 - - + +
28V LEU* 5.3 4.3 - - + -
42V ARG* 3.0 46.4 - - + +
43V VAL 3.3 1.0 + - - -
45V GLN* 1.3 87.9 - - - +
47V ARG* 1.3 53.0 + - - +
48V ARG 2.9 4.5 + - - -
49V GLU* 3.1 21.6 + - - +
50V VAL* 2.7 34.1 + - + +
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Residues in contact with ARG 47 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25V LEU* 3.2 37.9 - - + +
29V ARG* 5.4 7.9 - - - +
43V VAL* 3.1 23.3 - - + +
44V ARG* 3.0 16.1 + - - +
46V LEU* 1.3 77.2 - - - +
48V ARG* 1.3 56.3 + - - +
50V VAL* 4.1 6.7 - - - +
51V ALA 3.8 6.1 + - - -
58X C 4.9 4.0 + - - -
59X G 4.4 18.2 + - - -
70X A 6.0 0.4 - - - -
72X A 3.0 68.6 + - - +
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Residues in contact with ARG 48 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44V ARG 3.2 6.7 + - - +
45V GLN* 3.0 10.7 + - - +
46V LEU 2.9 0.4 - - - -
47V ARG* 1.3 76.0 - - - +
49V GLU* 1.3 57.4 + - - +
50V VAL 2.5 14.7 + - - -
51V ALA* 2.6 17.7 + - - +
52V GLN* 3.0 32.4 + - - +
74X G 4.3 5.1 + - - +
75X C 2.9 45.6 + - - -
76X C 5.1 4.0 + - - -
102X C 5.5 4.4 + - - -
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Residues in contact with GLU 49 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1V MET* 4.5 31.6 - - + +
21V ARG* 3.0 40.5 + - - +
42V ARG* 4.5 5.0 + - - -
45V GLN* 2.9 32.1 + - + +
46V LEU* 3.1 16.1 + - - +
48V ARG* 1.3 76.8 - - - +
50V VAL* 1.3 57.5 + - + +
52V GLN* 3.8 10.8 - - - +
53V LEU* 3.3 30.5 + - + +
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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