Contacts of the helix formed by residues 46 - 63 (chain K) in PDB entry 6T7B
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 ASN 46 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93I T 6.1 1.1 - - - -
94I G 5.3 12.3 - - - -
95I T 5.8 6.5 - - - -
53J A 5.1 11.5 + - - -
44K PRO 3.5 3.6 + - - -
45K MET* 1.3 74.4 - - - +
47K ALA* 1.3 68.5 + - - +
48K PHE 2.9 4.3 + - - -
49K MET* 3.0 7.2 + - - +
50K VAL* 2.9 20.3 + - - -
94K ALA* 5.0 2.2 - - - +
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Residues in contact with ALA 47 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94I G 5.0 10.2 + - - -
46K ASN* 1.3 72.2 - - - +
48K PHE* 1.3 55.8 + - - +
50K VAL* 4.2 1.1 - - - +
51K TRP* 3.0 24.9 + - - -
90K PHE* 3.9 29.1 - - - +
91K ILE* 4.9 4.3 - - - +
94K ALA* 4.7 7.0 - - - +
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Residues in contact with PHE 48 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93I T 5.3 13.1 + - - -
94I G 5.4 8.8 + - - -
46K ASN 3.1 1.2 - - - -
47K ALA* 1.3 75.5 - - - +
49K MET* 1.3 55.1 + - - +
51K TRP* 4.9 1.1 - - - +
52K SER* 2.6 34.5 + - - -
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Residues in contact with MET 49 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93I T 5.3 4.0 + - - -
53J A 5.9 10.4 - - - -
54J A 4.8 18.7 + - - +
45K MET* 5.3 3.1 - - - +
46K ASN* 3.0 12.4 + - - +
48K PHE* 1.3 75.2 - - - +
50K VAL* 1.3 63.1 + - - +
52K SER* 3.2 1.6 + - - +
53K ARG* 2.9 22.5 + - - -
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Residues in contact with VAL 50 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45K MET* 4.8 4.0 - - - +
46K ASN 2.9 14.4 + - - +
47K ALA* 4.2 1.1 - - - +
49K MET* 1.3 75.0 - - - +
51K TRP* 1.3 63.0 + - - +
53K ARG* 3.2 11.8 + - - +
54K GLY* 3.6 7.4 + - - -
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Residues in contact with TRP 51 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47K ALA 3.0 18.1 + - - -
48K PHE* 3.5 2.0 - - - +
50K VAL* 1.3 75.9 - - - +
52K SER* 1.3 56.7 + - - +
54K GLY* 4.4 0.2 - - - -
55K GLN* 3.0 23.6 + - - -
90K PHE* 6.4 1.1 - - - +
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Residues in contact with SER 52 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55J A 5.8 1.1 - - - +
48K PHE 2.6 20.7 + - - -
49K MET* 3.7 1.8 - - - +
51K TRP* 1.3 71.6 - - - +
53K ARG* 1.3 61.3 + - - +
54K GLY 3.2 0.4 - - - -
55K GLN* 4.6 0.4 - - - +
56K ARG* 2.4 37.0 + - - +
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Residues in contact with ARG 53 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54J A 5.4 8.2 + - - -
55J A 5.1 16.4 - - - +
49K MET 2.9 16.0 + - - -
50K VAL* 3.2 3.7 + - - +
52K SER* 1.3 79.3 - - - +
54K GLY* 1.3 58.9 + - - +
56K ARG* 4.4 0.2 - - - -
57K ARG* 3.5 13.0 + - - -
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Residues in contact with GLY 54 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50K VAL 3.6 8.9 + - - -
51K TRP 3.9 0.6 + - - -
52K SER 3.2 0.2 - - - -
53K ARG* 1.3 74.2 - - - +
55K GLN* 1.3 65.4 + - - +
57K ARG* 3.5 1.8 + - - -
58K LYS* 3.2 17.5 + - - -
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Residues in contact with GLN 55 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51K TRP 3.0 17.9 + - - -
52K SER* 4.6 0.7 - - - +
54K GLY* 1.3 73.9 - - - +
56K ARG* 1.3 66.7 + - - +
58K LYS* 2.9 3.6 + - - +
59K MET* 2.9 21.0 + - - -
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Residues in contact with ARG 56 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55J A 5.7 6.7 - - - -
56J G 4.5 8.4 + - - +
52K SER* 2.4 30.3 + - - +
53K ARG 4.4 0.2 - - - -
55K GLN* 1.3 66.7 - - - +
57K ARG* 1.3 60.8 + - - +
59K MET* 3.4 1.9 + - - +
60K ALA* 3.0 18.7 + - - -
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Residues in contact with ARG 57 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55J A 6.0 0.4 - - - -
56J G 4.3 12.6 + - - -
53K ARG 3.5 11.3 + - - -
54K GLY 3.5 5.2 + - - -
55K GLN 3.2 0.2 - - - -
56K ARG* 1.3 75.8 - - - +
58K LYS* 1.3 63.5 + - - +
60K ALA* 3.1 2.0 + - - +
61K GLN* 3.0 20.6 + - - -
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Residues in contact with LYS 58 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54K GLY 3.2 11.6 + - - -
55K GLN* 2.9 8.0 + - - +
57K ARG* 1.3 77.6 - - - +
59K MET* 1.3 61.4 + - - +
61K GLN* 3.4 1.4 + - - -
62K GLU* 3.2 18.2 + - - -
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Residues in contact with MET 59 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55K GLN 2.9 12.5 + - - -
56K ARG* 3.9 3.1 - - - +
58K LYS* 1.3 76.7 - - - +
60K ALA* 1.3 52.1 + - - +
62K GLU* 4.5 0.9 - - - +
63K ASN* 2.4 38.0 + - - +
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Residues in contact with ALA 60 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56J G 5.7 8.5 - - - -
56K ARG 3.0 15.6 + - - -
57K ARG* 3.1 4.2 + - - +
59K MET* 1.3 78.3 - - - +
61K GLN* 1.3 55.7 + - - +
63K ASN 3.6 9.0 - - - -
64K PRO* 2.5 35.2 - - - +
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Residues in contact with GLN 61 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57K ARG 3.0 13.3 + - - -
58K LYS 4.0 2.5 - - - -
60K ALA* 1.3 77.5 - - - +
62K GLU* 1.3 61.0 + - - +
64K PRO* 4.3 2.1 - - - +
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Residues in contact with GLU 62 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58K LYS 3.2 13.5 + - - -
59K MET* 3.5 1.8 - - - +
61K GLN* 1.3 77.0 - - - +
63K ASN* 1.3 58.0 + - - +
64K PRO 3.8 1.4 - - - -
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Residues in contact with ASN 63 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59K MET 2.4 27.3 + - - +
60K ALA* 3.0 9.4 - - - +
62K GLU* 1.3 72.1 - - - +
64K PRO* 1.3 59.3 - - - +
65K LYS 3.2 7.5 + - - +
66K MET* 3.3 18.8 + - - +
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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