Contacts of the helix formed by residues 48 - 64 (chain p) 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 GLU 48 (chain p).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47p PRO* 1.3 67.4 - - - +
49p VAL* 1.3 58.2 + - - +
51p ASN* 3.0 7.1 + - - +
52p ILE* 2.8 36.9 + - - +
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Residues in contact with VAL 49 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47p PRO 3.5 0.2 - - - -
48p GLU* 1.3 77.6 - - - +
50p ARG* 1.3 62.2 + - - +
52p ILE* 3.4 4.8 + - - +
53p VAL* 3.0 25.6 + - - +
90p TYR* 5.8 7.9 - - + -
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Residues in contact with ARG 50 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582M GLN* 5.0 9.6 - - + +
585M ASP* 4.5 21.3 - - + -
47p PRO* 3.6 11.8 + - + +
48p GLU 3.3 0.2 - - - -
49p VAL* 1.3 77.9 - - - +
51p ASN* 1.3 58.1 + - - +
53p VAL* 3.6 6.1 - - - +
54p ASP* 2.9 32.3 + - - +
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Residues in contact with ASN 51 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47p PRO 3.1 16.9 + - - +
48p GLU* 3.0 8.2 + - - +
50p ARG* 1.3 74.9 - - - +
52p ILE* 1.3 60.8 + - - +
54p ASP* 3.7 4.5 - - - +
55p LYS* 2.9 33.6 + - - +
109p PRO* 5.4 9.0 - - + -
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Residues in contact with ILE 52 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48p GLU 2.8 19.5 + - - +
49p VAL* 4.2 3.8 - - - +
51p ASN* 1.3 72.8 - - - +
53p VAL* 1.3 53.3 + - - +
55p LYS* 4.6 3.8 - - - -
56p THR* 2.8 38.4 + - - -
80p LYS 5.0 12.3 - - - +
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Residues in contact with VAL 53 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49p VAL 3.0 18.9 + - - +
50p ARG* 3.6 7.9 - - - +
52p ILE* 1.3 76.2 - - - +
54p ASP* 1.3 53.4 + - - +
56p THR* 3.7 2.9 - - - -
57p ALA* 2.8 38.6 + - - +
83p PHE* 5.6 10.1 - - + -
90p TYR* 5.7 8.5 - - + -
93p TYR* 5.9 2.0 - - + -
94p TYR* 4.6 23.9 - - + +
97p LYS* 5.2 1.8 - - + -
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Residues in contact with ASP 54 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50p ARG 2.9 19.5 + - - +
51p ASN* 3.7 6.1 - - - +
53p VAL* 1.3 76.0 - - - +
55p LYS* 1.3 55.7 + - - +
57p ALA* 3.4 7.1 + - - +
58p SER* 2.9 27.8 + - - -
97p LYS* 4.6 9.0 - - + +
109p PRO* 5.3 11.7 - - + -
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Residues in contact with LYS 55 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51p ASN 2.9 21.2 + - - +
52p ILE* 4.1 4.3 - - - +
54p ASP* 1.3 70.4 - - - +
56p THR* 1.3 66.3 + - - +
58p SER* 3.2 8.8 + - - -
59p PHE* 3.2 21.1 + - - +
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Residues in contact with THR 56 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52p ILE* 2.8 24.6 + - - -
53p VAL* 3.8 3.4 - - - -
55p LYS* 1.3 71.4 - - - +
57p ALA* 1.3 61.9 + - - +
59p PHE* 3.2 7.7 + - - +
60p VAL* 3.0 25.3 + - - +
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Residues in contact with ALA 57 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53p VAL 2.8 21.7 + - - +
54p ASP 3.5 2.7 - - - +
56p THR* 1.3 72.8 - - - +
58p SER* 1.3 51.5 + - - +
60p VAL* 3.3 6.7 + - - +
61p ALA* 2.7 37.9 + - - +
94p TYR* 4.2 8.3 - - + +
97p LYS* 3.4 31.4 - - + -
98p VAL* 3.7 16.3 - - + +
101p PHE* 4.9 0.9 - - + -
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Residues in contact with SER 58 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54p ASP 2.9 14.0 + - - -
55p LYS* 3.3 13.5 - - - -
57p ALA* 1.3 74.4 - - - +
59p PHE* 1.3 57.3 + - - +
61p ALA* 3.0 9.6 + - - +
62p ARG* 2.9 29.2 + - - +
101p PHE* 4.1 12.9 - - - +
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Residues in contact with PHE 59 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55p LYS 3.2 9.4 + - - +
56p THR* 3.2 9.2 + - - +
58p SER* 1.3 78.6 - - - +
60p VAL* 1.3 57.0 + - - +
62p ARG* 3.3 4.6 + - - +
63p ASN* 2.9 34.0 + - - +
67p PHE* 5.2 3.6 - - + -
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Residues in contact with VAL 60 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56p THR 3.0 17.7 + - - +
57p ALA* 3.8 6.1 - - - +
59p PHE* 1.3 74.4 - - - +
61p ALA* 1.3 58.5 + - - +
64p GLY* 2.9 43.9 + - - +
65p PRO* 3.7 2.0 - - + +
67p PHE* 4.3 7.4 - - + +
68p GLU* 4.4 22.9 - - + +
98p VAL* 5.6 6.1 - - + -
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Residues in contact with ALA 61 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57p ALA 2.7 21.0 + - - +
58p SER 3.0 6.0 + - - +
60p VAL* 1.3 75.7 - - - +
62p ARG* 1.3 61.9 + - - +
64p GLY* 4.0 3.8 + - - -
98p VAL* 3.3 29.6 - - - +
101p PHE* 3.5 18.8 - - + -
102p LYS* 3.9 17.8 - - - +
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Residues in contact with ARG 62 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58p SER 2.9 14.5 + - - +
59p PHE* 3.9 5.4 - - - +
61p ALA* 1.3 79.3 - - - +
63p ASN* 1.3 61.9 + - - +
64p GLY* 3.4 1.0 + - - -
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Residues in contact with ASN 63 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59p PHE 2.9 19.2 + - - +
62p ARG* 1.3 72.5 - - - +
64p GLY* 1.3 59.0 + - - +
66p GLU* 5.0 7.1 - - - +
67p PHE* 4.6 14.1 + - + -
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Residues in contact with GLY 64 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60p VAL* 2.9 21.2 + - - +
61p ALA 4.0 3.1 + - - -
62p ARG 3.3 4.2 + - - -
63p ASN* 1.3 79.1 - - - +
65p PRO* 1.3 59.0 - - - +
66p GLU* 3.0 12.5 + - - -
67p PHE* 3.1 16.3 + - - +
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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