Contacts of the helix formed by residues 17 - 31 (chain B) in PDB entry 4Q3F
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 GLY 17 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B PRO 3.4 0.4 + - - -
16B ALA* 1.3 72.2 - - - +
18B LEU* 1.3 64.5 + - - +
19B GLU* 3.2 18.6 + - - -
20B LYS* 3.1 21.1 + - - +
21B ARG* 3.2 23.1 + - - +
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Residues in contact with LEU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LEU* 3.9 27.1 - - + -
14B VAL* 3.7 25.4 - - + -
15B PRO* 3.3 21.1 + - + +
16B ALA 3.4 0.6 - - - -
17B GLY* 1.3 77.2 - - - +
19B GLU* 1.4 60.9 + - - +
21B ARG* 3.3 10.6 + - - +
22B LEU* 2.8 34.1 + - + +
41B VAL* 4.3 11.0 - - + -
83B PHE* 4.2 12.8 - - + -
84B LEU* 4.7 3.8 - - + -
87B GLU* 3.7 40.2 - - + +
88B LEU* 4.1 7.4 - - + -
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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 PRO 5.3 0.3 - - - +
17B GLY* 3.9 15.5 + - - -
18B LEU* 1.4 81.4 + - - +
20B LYS* 1.3 62.4 + - + +
22B LEU 3.9 0.2 - - - -
23B CYS* 3.0 28.4 + - - +
39B VAL* 3.7 36.0 - - + +
41B VAL* 4.3 14.1 - - + +
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Residues in contact with LYS 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLY* 3.1 14.1 + - - +
19B GLU* 1.3 82.6 - - + +
21B ARG* 1.3 65.6 + - + +
23B CYS* 3.2 10.2 - - + +
24B ALA* 3.1 21.5 + - - +
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Residues in contact with ARG 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PRO* 3.7 12.7 - - - +
16B ALA 2.9 28.7 + - - -
17B GLY* 3.2 16.1 + - - +
18B LEU* 3.5 15.9 - - - +
20B LYS* 1.3 79.2 - - + +
22B LEU* 1.3 60.8 + - - +
24B ALA* 3.3 7.3 + - - +
25B ALA* 3.0 28.2 + - - +
83B PHE* 3.6 16.7 - - + -
87B GLU* 2.7 39.5 + - - -
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Residues in contact with LEU 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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3B LEU* 4.0 15.0 - - + -
5B LEU* 4.6 16.4 - - + -
18B LEU* 2.8 23.3 + - + +
19B GLU 4.0 2.9 - - - +
21B ARG* 1.3 74.3 - - - +
23B CYS* 1.3 61.0 + - - +
25B ALA* 4.2 1.6 - - + -
26B ALA* 2.9 32.9 + - - +
39B VAL* 3.7 24.2 - - + -
59B LEU* 4.7 9.2 - - + -
80B PHE* 4.0 26.5 - - + -
83B PHE* 3.7 32.0 - - + -
84B LEU* 4.5 17.7 - - + -
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Residues in contact with CYS 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 GLU 3.0 20.9 + - - +
20B LYS* 3.2 14.1 - - + +
22B LEU* 1.3 78.6 - - - +
24B ALA* 1.3 61.6 + - - +
27B ALA* 3.2 21.1 + - - +
34B ALA* 3.9 12.5 - - - +
37B VAL* 3.7 39.5 - - - +
39B VAL* 3.8 13.4 - - + +
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Residues in contact with ALA 24 (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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74A ARG* 6.6 0.4 - - - -
20B LYS 3.1 13.8 + - - +
21B ARG* 3.3 9.4 + - - +
23B CYS* 1.3 75.8 - - - +
25B ALA* 1.3 63.2 + - - +
27B ALA* 3.4 8.5 + - - +
28B SER* 3.3 23.7 + - - -
34B ALA* 5.2 7.2 - - + -
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Residues in contact with ALA 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ARG 3.0 18.0 + - - +
22B LEU* 3.8 5.8 - - + +
24B ALA* 1.3 77.6 - - - +
26B ALA* 1.3 56.8 + - - +
28B SER* 3.2 7.3 + - - -
29B ILE* 2.8 44.2 + - + +
83B PHE* 3.8 32.8 - - + -
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Residues in contact with ALA 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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3B LEU* 3.6 36.1 - - + -
22B LEU 2.9 18.6 + - - +
23B CYS 4.0 3.1 - - - +
25B ALA* 1.3 75.6 - - - +
27B ALA* 1.3 58.6 + - - +
30B LEU* 2.9 37.6 + - + +
32B LYS* 5.2 0.3 - - - +
37B VAL* 4.0 9.9 - - + -
80B PHE* 3.8 16.8 - - + -
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Residues in contact with ALA 27 (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 CYS 3.2 11.1 + - - +
24B ALA 3.4 8.9 + - - +
26B ALA* 1.3 73.5 - - - +
28B SER* 1.3 57.7 + - - +
31B GLY* 2.9 24.8 + - - -
32B LYS* 2.9 31.3 + - - +
34B ALA* 3.6 30.3 - - + +
37B VAL* 3.9 8.1 - - + +
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Residues in contact with SER 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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92A GLN* 3.0 22.3 + - - +
24B ALA 3.3 10.4 + - - -
25B ALA* 3.2 10.3 + - - -
27B ALA* 1.3 79.9 - - - +
29B ILE* 1.3 66.0 + - - +
30B LEU 3.5 0.2 + - - -
31B GLY* 3.5 2.3 + - - -
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Residues in contact with ILE 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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92A GLN* 3.0 16.8 - - - +
25B ALA* 2.8 33.2 + - + +
26B ALA 4.0 0.9 - - - +
28B SER* 1.3 74.1 - - - +
30B LEU* 1.3 59.2 + - - +
76B HIS* 3.7 38.5 + - - +
79B HIS* 3.5 43.8 - - + +
80B PHE* 3.5 49.8 - - + -
83B PHE* 5.2 2.2 - - + -
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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
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92A GLN* 4.7 1.3 - - - -
1B PRO* 3.9 24.9 - - + -
3B LEU* 4.5 5.4 - - + -
26B ALA 2.9 19.5 + - - +
29B ILE* 1.3 76.2 - - - +
31B GLY* 1.3 64.4 + - - +
32B LYS* 3.7 16.2 - - + +
61B ILE* 3.9 22.7 - - + -
63B SER* 4.9 2.5 - - - -
66B VAL* 3.8 24.4 - - + +
67B VAL* 3.7 17.5 - - + -
76B HIS* 3.7 38.0 - - + +
80B PHE* 4.3 20.2 - - + -
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Residues in contact with GLY 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A GLN* 3.7 22.2 - - - +
27B ALA 2.9 9.3 + - - -
28B SER* 3.5 0.8 + - - -
29B ILE 3.3 3.4 + - - -
30B LEU* 1.3 80.8 - - - +
32B LYS* 1.3 66.0 + - - +
33B PRO* 4.8 0.2 - - - +
66B VAL* 5.7 0.3 - - - +
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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