Contacts of the helix formed by residues 40 - 63 (chain w) in PDB entry 6FF7
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 w).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180o LYS* 2.4 9.0 - - - +
181o GLY* 0.4 186.4 + - - +
182o PHE* 1.3 101.7 + - + +
183o GLY 3.7 0.4 - - - +
39w LEU* 1.3 68.5 - - - -
41w LYS* 1.3 26.9 - - - +
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Residues in contact with LYS 41 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180o LYS* 2.1 32.4 - - - +
181o GLY* 1.4 43.1 + - - -
39w LEU 3.1 4.2 - - - +
40w PRO* 1.3 60.0 - - - +
42w ALA* 1.3 54.7 + - - +
45w TRP* 3.2 11.0 + - - +
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Residues in contact with ALA 42 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178o HIS 2.4 4.5 - - - +
179o GLU* 2.0 33.9 - - - +
181o GLY* 2.0 11.5 - - - -
39w LEU* 3.3 13.7 + - - +
41w LYS* 1.3 66.1 - - - +
43w GLU* 1.3 46.8 + - - +
45w TRP* 3.9 6.9 - - - +
46w ARG* 3.2 8.3 + - - +
87w TRP* 4.4 12.0 - - + +
90w ARG* 5.1 6.5 - - + -
91w ILE* 4.4 23.3 - - + +
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Residues in contact with GLU 43 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174o CYS* 3.5 9.2 - - - +
178o HIS* 1.2 181.7 + - + +
179o GLU* 1.0 98.7 + - - +
180o LYS* 0.7 45.7 + - + +
181o GLY 2.2 15.7 - - - +
182o PHE 3.1 17.0 - - - +
42w ALA* 1.3 52.5 - - - +
44w LYS* 2.2 7.5 + - - +
47w ARG* 3.8 4.2 + - - +
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Residues in contact with LYS 44 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179o GLU 1.7 7.9 - - - -
180o LYS* 0.7 271.0 - - + +
214o ILE* 5.5 2.2 - - + +
43w GLU 1.3 7.5 - - - -
45w TRP* 1.3 59.4 + - - +
47w ARG* 3.3 8.0 + - - +
48w GLN* 3.2 21.4 + - - +
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Residues in contact with TRP 45 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179o GLU 1.8 14.0 + - - +
180o LYS* 2.8 2.2 - - - +
41w LYS 3.2 10.0 + - - +
42w ALA* 3.9 7.4 - - - +
44w LYS* 1.3 72.2 - - - +
46w ARG* 1.3 60.7 + - - +
48w GLN* 3.6 7.6 + - - +
49w ILE* 3.5 19.1 + - - +
87w TRP* 4.9 8.8 - - + +
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Residues in contact with ARG 46 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179o GLU* 2.2 55.4 + - + -
42w ALA 3.2 4.4 + - - +
45w TRP* 1.3 68.0 - - - +
47w ARG* 1.3 59.3 + - - -
49w ILE* 3.4 13.8 + - - +
50w ILE* 3.4 11.8 + - - +
84w LYS* 5.5 7.2 - - + +
87w TRP* 4.1 20.2 - - + +
88w GLU* 4.5 14.8 - - + +
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Residues in contact with ARG 47 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174o CYS* 4.6 16.2 - - + -
179o GLU* 3.3 5.0 - - + +
43w GLU 4.2 7.0 - - - +
44w LYS* 3.3 9.8 + - - +
46w ARG* 1.3 75.8 - - - +
48w GLN* 1.3 65.6 + - - +
50w ILE* 3.0 19.3 + - - +
51w GLY* 3.3 9.4 + - - -
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Residues in contact with GLN 48 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44w LYS 3.2 13.3 + - - +
45w TRP* 3.9 9.4 - - - +
46w ARG 3.3 0.2 - - - -
47w ARG* 1.3 80.9 - - - +
49w ILE* 1.3 60.6 + - - +
51w GLY* 3.3 9.9 + - - -
52w GLU* 3.5 10.6 + - - +
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Residues in contact with ILE 49 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45w TRP 3.5 8.7 + - - +
46w ARG* 3.4 11.1 + - - +
47w ARG 3.2 0.8 - - - -
48w GLN* 1.3 75.0 - - - +
50w ILE* 1.3 66.4 + - - +
52w GLU* 3.1 17.8 + - - +
53w ILE* 3.1 12.6 + - - +
80w LEU* 4.5 21.0 - - + +
83w GLU* 5.2 9.4 - - + -
84w LYS* 5.2 9.6 - - + +
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Residues in contact with ILE 50 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46w ARG 3.4 8.4 + - - +
47w ARG* 3.0 14.4 + - - +
49w ILE* 1.3 79.0 - - - +
51w GLY* 1.3 62.3 + - - +
53w ILE* 3.1 17.1 + - - +
54w SER* 3.1 13.7 + - - -
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Residues in contact with GLY 51 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47w ARG 3.3 7.8 + - - -
48w GLN* 3.3 4.4 + - - -
49w ILE 3.2 0.8 - - - -
50w ILE* 1.3 79.3 - - - +
52w GLU* 1.3 62.2 + - - +
54w SER* 3.3 7.5 + - - -
55w LYS* 3.1 21.1 + - - +
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Residues in contact with GLU 52 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48w GLN 3.5 9.5 + - - +
49w ILE* 3.1 11.9 + - - +
51w GLY* 1.3 74.0 - - - +
53w ILE* 1.3 65.5 + - - +
55w LYS* 3.1 8.2 + - - +
56w LYS* 3.1 21.5 + - - +
80w LEU* 5.3 7.2 - - + -
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Residues in contact with ILE 53 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49w ILE 3.1 11.9 + - - +
50w ILE* 3.1 10.7 + - - +
52w GLU* 1.3 74.5 - - - +
54w SER* 1.3 52.8 + - - +
56w LYS* 3.1 9.4 + - - +
57w VAL* 2.8 34.0 + - - +
77w ILE* 5.4 11.0 - - + +
80w LEU* 4.6 17.0 - - + +
81w LEU* 5.8 1.6 - - - +
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Residues in contact with SER 54 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50w ILE 3.1 9.5 + - - -
51w GLY* 3.6 10.3 - - - -
53w ILE* 1.3 77.8 - - - +
55w LYS* 1.3 66.6 + - - +
57w VAL* 2.9 18.7 + - - +
58w ALA* 3.1 12.8 + - - +
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Residues in contact with LYS 55 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51w GLY 3.1 13.9 + - - +
52w GLU* 3.1 11.9 + - - +
54w SER* 1.3 77.6 - - - +
56w LYS* 1.3 63.1 + - - +
58w ALA* 3.6 14.4 + - - +
59w GLN* 3.8 5.9 + - - +
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Residues in contact with LYS 56 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52w GLU 3.1 8.7 + - - +
53w ILE* 3.1 10.9 + - - +
54w SER 3.1 0.4 - - - -
55w LYS* 1.3 78.9 - - - +
57w VAL* 1.4 64.9 + - - +
58w ALA 3.1 0.2 - - - -
59w GLN* 3.1 16.8 + - - +
60w ILE* 3.3 10.9 + - - +
73w LEU* 4.6 24.1 - - + +
76w GLU* 5.7 4.5 - - + -
77w ILE* 5.2 11.4 - - + +
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Residues in contact with VAL 57 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53w ILE 2.8 16.9 + - - +
54w SER* 2.9 12.2 + - - +
56w LYS* 1.4 73.7 - - - +
58w ALA* 1.3 57.1 + - - +
60w ILE* 3.1 10.5 + - - +
61w GLN* 2.8 27.4 + - - +
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Residues in contact with ALA 58 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54w SER 3.1 10.4 + - - +
55w LYS* 3.8 11.2 - - - +
56w LYS 3.1 0.4 - - - -
57w VAL* 1.3 77.0 - - - +
59w GLN* 1.3 63.5 + - - +
61w GLN* 2.9 19.8 + - - +
62w ASN* 2.9 12.6 + - - +
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Residues in contact with GLN 59 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55w LYS 3.8 5.8 + - - +
56w LYS* 3.1 12.5 + - - +
58w ALA* 1.3 78.4 - - - +
60w ILE* 1.3 61.9 + - - +
62w ASN* 3.3 20.1 + - - +
63w ALA* 3.6 3.6 + - - -
65w LEU* 5.0 14.4 - - + +
70w ILE* 6.2 0.2 - - - -
73w LEU* 5.2 9.0 - - + -
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Residues in contact with ILE 60 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56w LYS 3.3 7.4 + - - +
57w VAL* 3.1 13.6 + - - +
58w ALA 3.1 0.2 - - - -
59w GLN* 1.3 77.0 - - - +
61w GLN* 1.3 64.8 + - - +
63w ALA* 3.1 17.0 + - - +
70w ILE* 5.5 14.1 - - + +
73w LEU* 5.1 11.6 - - + +
74w ASN* 6.0 3.8 - - + +
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Residues in contact with GLN 61 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57w VAL 2.8 12.8 + - - +
58w ALA* 3.2 13.0 - - - +
60w ILE* 1.3 76.5 - - - +
62w ASN* 1.3 64.5 + - - +
63w ALA* 3.3 4.7 + - - +
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Residues in contact with ASN 62 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58w ALA 2.9 10.1 + - - +
59w GLN* 3.4 15.0 - - - +
60w ILE 3.1 0.4 - - - -
61w GLN* 1.3 78.6 - - - +
63w ALA* 1.4 73.3 + - - +
64w GLY* 4.4 3.0 - - - +
65w LEU* 5.4 3.4 - - + +
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Residues in contact with ALA 63 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59w GLN 3.6 3.6 + - - -
60w ILE* 3.1 16.5 + - - +
61w GLN 4.0 4.5 - - - +
62w ASN* 1.4 85.8 - - - +
64w GLY* 1.3 57.9 + - - +
65w LEU* 6.0 0.2 - - - -
70w ILE* 6.3 2.9 - - - -
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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
------------------------------------------------------------
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) + - + + + + + -
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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