Contacts of the helix formed by residues 62 - 73 (chain B) in PDB entry 4KPE
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 SER 62 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B ARG 3.1 3.9 + - - -
61B LYS* 1.3 72.4 - - - +
63B ALA* 1.3 62.4 + - - +
65B SER* 3.0 19.1 + - - -
66B VAL* 3.0 15.3 + - - +
82B TYR* 3.8 17.3 - - - -
85B MET* 4.6 5.3 - - - +
101B MET* 4.2 3.6 - - - +
116B MET* 3.6 7.4 - - - -
119B THR* 2.8 45.4 + - - -
120B GLU 3.9 8.7 - - - -
121B ALA* 3.9 9.6 - - - +
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Residues in contact with ALA 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLY* 3.7 12.8 - - - -
70A MET* 3.7 35.2 - - + -
78A ASP* 5.1 0.2 - - + -
61B LYS* 3.3 2.6 - - + -
62B SER* 1.3 79.4 - - - +
64B LYS* 1.3 57.1 + - - +
66B VAL* 3.9 1.7 - - - +
67B GLY* 3.1 23.0 + - - -
116B MET* 3.4 43.1 + - + +
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Residues in contact with LYS 64 (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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64A LYS 5.7 0.3 - - - +
67A GLY* 3.4 24.8 + - - +
68A ASN* 3.6 22.1 - - - +
71A GLY* 4.2 15.7 + - - -
72A ASN* 3.0 31.0 + - - +
60B ARG* 3.8 45.0 - - + +
61B LYS* 3.0 15.3 + - + +
63B ALA* 1.3 76.0 - - - +
65B SER* 1.3 65.7 + - - +
67B GLY* 4.3 0.2 - - - -
68B ASN* 3.3 36.3 + - - +
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Residues in contact with SER 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B SER* 4.8 0.3 + - - -
48B MET* 4.4 21.6 - - - +
51B ASP* 5.8 1.8 - - - -
53B ASN* 3.5 22.3 + - - -
60B ARG* 3.5 13.3 + - - +
61B LYS 3.9 4.5 + - - -
62B SER* 3.0 9.0 + - - -
64B LYS* 1.3 76.4 - - - +
66B VAL* 1.3 67.1 + - - +
68B ASN* 3.3 6.9 + - - +
69B ILE* 3.0 30.1 + - - +
85B MET* 4.5 12.9 - - - -
121B ALA* 5.1 1.7 + - - +
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Residues in contact with VAL 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B SER 3.0 16.6 + - - +
63B ALA 4.0 3.6 - - - +
65B SER* 1.3 78.3 - - - +
67B GLY* 1.3 58.4 + - - +
69B ILE* 3.2 11.5 + - + +
70B MET* 2.9 48.0 + - + +
78B ASP* 3.8 19.7 - - + +
81B ILE* 4.2 10.0 - - + +
82B TYR* 3.9 41.1 - - + +
85B MET* 4.4 9.4 - - - -
116B MET* 4.0 12.8 - - - -
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Residues in contact with GLY 67 (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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63A ALA* 3.7 24.2 - - - -
64A LYS* 3.6 17.7 + - - +
67A GLY* 5.4 0.4 - - - -
63B ALA 3.1 15.0 + - - -
64B LYS 4.3 0.2 - - - -
66B VAL* 1.3 81.0 - - - +
68B ASN* 1.3 57.6 + - - +
70B MET* 3.4 8.9 + - - +
71B GLY 3.0 23.0 + - - -
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Residues in contact with ASN 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LYS* 3.4 27.0 + - - +
68A ASN* 3.7 20.7 + - - +
47B SER* 4.2 2.9 + - - +
51B ASP* 3.6 34.9 + - - +
60B ARG* 5.1 1.6 - - - +
64B LYS* 3.3 30.8 + - - +
65B SER* 3.6 5.6 - - - +
66B VAL 3.3 0.4 - - - -
67B GLY* 1.3 73.8 - - - +
69B ILE* 1.3 64.9 + - - +
71B GLY 3.3 0.5 + - - -
72B ASN* 3.0 38.8 + - - +
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Residues in contact with ILE 69 (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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40B VAL* 5.8 0.2 - - + -
43B ARG* 4.5 12.6 - - + -
44B ILE* 3.6 39.5 - - + +
47B SER* 3.6 27.1 - - - -
48B MET* 4.9 1.6 - - + +
65B SER* 3.0 30.2 + - - +
66B VAL* 3.3 7.9 - - + +
68B ASN* 1.3 74.8 - - - +
70B MET* 1.3 59.2 + - - +
73B PHE* 2.8 30.2 + - + -
74B HIS* 2.9 27.5 + - + +
81B ILE* 3.7 25.4 - - + -
85B MET* 5.4 1.8 - - - -
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Residues in contact with MET 70 (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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61A LYS* 4.3 20.2 - - + +
63A ALA* 3.7 26.2 - - + -
117A ARG* 4.3 15.9 - - - +
66B VAL* 2.9 24.3 + - + +
67B GLY* 3.6 5.2 - - - +
69B ILE* 1.3 77.4 - - - +
71B GLY* 1.3 58.7 + - - +
74B HIS 3.3 18.3 - - - +
75B PRO* 4.5 2.8 - - + +
76B HIS 3.8 19.5 - - - +
78B ASP* 3.0 46.4 - - + +
81B ILE* 3.9 7.6 - - + -
145B PHE* 3.9 12.0 - - - -
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Residues in contact with GLY 71 (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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61A LYS* 4.3 17.3 - - - -
64A LYS* 4.0 14.3 + - - +
67B GLY 3.0 15.5 + - - -
68B ASN 3.3 1.3 + - - -
69B ILE 3.3 0.2 - - - -
70B MET* 1.3 77.8 - - - +
72B ASN* 1.3 68.3 + - - +
145B PHE* 3.6 13.4 - - - -
146B ASP* 3.8 12.5 - - - +
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Residues in contact with ASN 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LYS* 3.1 32.4 + - - +
47B SER* 5.1 1.4 + - - -
50B LYS* 6.2 1.0 - - - +
51B ASP* 5.4 3.8 + - - -
68B ASN* 3.0 27.6 + - - +
71B GLY* 1.3 83.8 - - - +
73B PHE* 1.3 82.8 + - + +
144B ASN* 2.9 29.5 + - - +
145B PHE* 3.9 3.6 - - - -
146B ASP* 5.4 0.2 - - - -
149B GLU* 3.4 22.7 + - - +
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Residues in contact with PHE 73 (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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43B ARG* 3.3 42.1 + - + +
46B TYR* 3.6 30.5 - + - -
47B SER* 3.7 37.2 - - - -
50B LYS* 4.5 5.8 - - + -
69B ILE* 2.8 17.6 + - - +
72B ASN* 1.3 93.5 - - + +
74B HIS* 1.3 57.8 + - - +
75B PRO* 3.3 9.9 - - - +
144B ASN* 4.7 2.5 - - + -
145B PHE* 3.6 13.3 - - - -
149B GLU* 3.6 35.7 - - + -
150B LYS 4.1 4.7 - - - -
151B GLU* 3.7 32.1 - - + +
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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