Contacts of the helix formed by residues 41 - 53 (chain A) in PDB entry 4K2S
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 ARG 41 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 3.0 25.0 + - + +
39A ASN 3.2 0.4 - - - +
40A GLY* 1.3 95.0 + - - +
42A GLU* 1.3 65.3 + - - +
44A ALA* 3.1 17.4 + - + +
45A VAL* 3.8 6.6 + - - +
179A PRO* 6.2 1.0 - - - +
391A SER* 4.9 10.3 + - - -
392A LEU 6.0 0.2 - - - +
48B TYR* 3.0 48.9 + - + +
52B HIS* 3.2 43.9 + - + +
53B VAL* 4.7 5.7 - - - +
72B LEU* 4.4 13.5 + - - +
75B GLY 4.5 3.0 + - - -
76B ALA* 3.6 33.8 - - + +
78B TRP* 4.6 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ARG* 3.0 25.3 + - - -
18A ASN* 3.8 28.0 + - + +
20A VAL* 4.0 21.0 - - + +
37A THR* 4.4 7.9 - - + -
38A LEU* 3.4 22.0 - - - +
39A ASN* 3.4 2.3 - - - +
40A GLY* 3.1 31.6 + - - -
41A ARG* 1.3 79.2 + - - +
43A MET* 1.3 63.6 + - - +
44A ALA 3.3 0.5 + - - -
45A VAL* 3.3 6.9 + - - +
46A ALA* 3.2 18.9 + - - +
387A TYR* 4.4 15.1 + - + -
390A ALA 4.5 3.9 + - - +
52B HIS* 3.2 8.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A VAL* 4.4 17.5 - - + -
20A VAL* 5.5 0.4 - - - -
42A GLU* 1.3 77.4 - - - +
44A ALA* 1.3 59.8 + - - +
46A ALA* 3.7 19.4 - - + +
47A ALA* 3.0 23.3 + - - +
387A TYR* 3.9 35.0 - - + -
47B ALA* 3.4 16.0 - - + +
51B GLU* 3.5 32.1 - - + -
52B HIS* 3.0 10.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ARG 3.1 13.2 + - - +
43A MET* 1.3 80.2 - - - +
45A VAL* 1.3 56.9 + - - +
47A ALA* 3.5 0.7 + - - +
48A TYR* 3.0 26.9 + - - +
83A VAL* 3.7 15.2 - - + +
44B ALA* 3.9 15.2 - - - +
47B ALA* 4.2 3.8 - - - +
48B TYR* 3.7 42.6 - - + -
52B HIS* 4.0 4.0 + - + -
83B VAL* 4.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ALA* 3.4 35.2 - - + +
38A LEU* 3.7 40.4 - - + -
41A ARG 3.8 2.2 + - - +
42A GLU 3.3 5.9 + - - +
44A ALA* 1.3 75.0 - - - +
46A ALA* 1.3 65.8 + - - +
48A TYR* 3.2 1.8 + - - +
49A LEU* 2.9 26.0 + - + +
83A VAL* 3.9 17.0 - - + -
86A THR* 4.0 7.2 - - + -
87A ALA* 3.9 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A THR* 4.8 4.0 - - - +
12A VAL* 4.5 15.3 - - + -
20A VAL* 4.5 13.8 - - + +
42A GLU 3.2 11.6 + - - +
43A MET* 3.7 31.4 - - + +
45A VAL* 1.3 78.4 - - - +
47A ALA* 1.3 57.7 + - - +
49A LEU* 3.8 4.0 - - - +
50A ASP* 2.8 43.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A MET 3.0 17.7 + - - +
44A ALA 4.0 2.5 - - - +
46A ALA* 1.3 72.5 - - - +
48A TYR* 1.3 66.8 + - - +
50A ASP* 4.4 6.5 - - - +
51A GLU* 3.0 30.0 + - + +
52A HIS* 3.9 1.4 - - - -
43B MET* 3.5 29.6 - - + +
44B ALA* 4.6 2.2 - - - -
47B ALA* 3.6 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ALA 3.0 18.9 + - - +
45A VAL* 3.5 5.8 - - - +
47A ALA* 1.3 75.5 - - - +
49A LEU* 1.3 61.8 + - - +
52A HIS* 3.2 12.2 + - - +
53A VAL* 3.2 32.5 + - + -
72A LEU 5.0 0.7 + - - -
76A ALA* 3.5 19.4 - - - +
78A TRP 4.9 0.3 + - - -
83A VAL* 3.8 16.2 - - + -
84A THR* 3.5 33.6 + - - +
87A ALA* 3.4 24.2 - - + -
88A ILE* 5.5 3.8 - - + +
38B LEU* 5.8 0.4 - - + -
41B ARG* 3.0 42.5 + - + +
44B ALA* 3.7 25.2 - - + +
82B PRO* 6.1 0.4 - - + -
83B VAL* 4.1 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A THR* 3.8 23.6 - - + -
20A VAL* 5.1 0.7 - - + -
22A LEU* 4.3 14.1 - - + -
36A ALA* 3.7 30.3 - - + -
45A VAL* 2.9 21.1 + - + +
46A ALA 3.8 3.1 - - - +
48A TYR* 1.3 75.8 - - - +
50A ASP* 1.3 61.7 + - - +
53A VAL* 3.2 24.7 + - + -
54A VAL* 2.8 34.5 + - + +
87A ALA* 3.7 33.4 - - + +
90A ALA* 4.2 7.4 - - + -
91A VAL* 4.2 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TYR* 5.2 0.3 - - - -
10A THR* 2.8 37.3 + - - +
46A ALA* 2.8 31.4 + - - +
47A ALA* 4.2 4.7 - - - +
49A LEU* 1.3 74.0 - - - +
51A GLU* 1.3 61.4 + - + +
54A VAL* 4.1 10.1 - - - +
55A PRO* 3.6 14.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ALA* 3.0 16.6 + - - +
50A ASP* 1.3 79.9 - - + +
52A HIS* 1.3 84.3 + - + +
55A PRO* 3.8 6.4 - - - +
43B MET* 3.5 17.7 - - + +
387B TYR* 2.7 35.1 + - - +
389B ARG* 3.3 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ALA 3.9 8.7 - - - -
48A TYR* 3.2 12.5 + - - +
51A GLU* 1.3 107.5 + - + +
53A VAL* 1.3 65.4 + - - +
55A PRO* 4.0 4.9 - - - +
56A ALA* 4.3 10.2 + - - +
40B GLY 3.1 15.1 + - - -
41B ARG* 3.2 47.6 + - + +
42B GLU* 3.4 19.7 - - - -
43B MET* 2.9 25.1 + - - +
44B ALA 4.2 4.5 - - - -
178B LEU* 6.0 0.5 - - - +
387B TYR* 3.4 14.8 + - - -
389B ARG* 5.1 5.7 - - + +
390B ALA 5.8 0.6 + - - -
391B SER* 5.1 8.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A TYR* 3.2 40.7 + - + +
49A LEU* 3.8 19.3 - - + +
52A HIS* 1.3 80.4 - - - +
54A VAL* 1.3 67.9 + - - +
55A PRO 3.3 0.4 - - - -
56A ALA* 3.0 17.2 + - - +
57A LEU* 3.2 17.9 + - + +
72A LEU* 4.0 30.1 - - + -
87A ALA* 4.7 2.2 - - + -
88A ILE* 6.3 0.9 - - + -
91A VAL* 3.9 27.6 - - + -
41B ARG* 4.6 4.3 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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