Contacts of the helix formed by residues 59 - 71 (chain K) in PDB entry 4XLQ
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 59 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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693J GLU 5.6 0.6 + - - -
694J VAL 4.3 6.5 + - - -
696J HIS 2.8 22.2 + - - +
697J GLY* 3.5 3.3 - - - -
698J LYS* 3.1 53.9 + - - +
57K ASP* 3.0 22.9 - - - +
58K PRO* 1.3 80.1 - - + +
60K ALA* 1.3 64.8 - - - +
61K VAL* 3.3 20.7 + - - +
62K THR* 3.4 6.9 + - - +
63K TRP* 3.2 22.9 + - - -
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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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698J LYS* 5.2 5.7 - - - +
753J SER* 4.8 4.3 - - - +
27K ALA* 3.3 36.2 - - + +
30K LEU* 3.7 3.2 - - + +
31K LEU* 3.6 29.4 - - + +
35K PHE* 4.9 1.3 - - - -
58K PRO 3.0 6.9 + - - -
59K ASN* 1.3 70.0 - - - +
61K VAL* 1.3 68.6 + - + +
63K TRP* 3.0 12.6 - - - +
64K ALA 2.9 19.9 + - - -
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Residues in contact with VAL 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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698J LYS* 4.2 7.9 - - + -
753J SER* 4.7 7.9 - - - +
756J GLN* 3.6 30.5 - - + -
757J ALA* 4.3 17.0 - - + +
760J ARG* 3.3 34.8 - - + +
761J ILE* 6.2 0.7 - - + -
23K VAL* 4.0 7.4 - - + +
27K ALA* 4.1 10.3 - - + -
59K ASN* 3.3 15.5 - - - +
60K ALA* 1.3 79.8 - - + +
62K THR* 1.3 57.4 + - - +
64K ALA* 3.2 3.7 + - - +
65K MET* 2.9 35.6 + - + +
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Residues in contact with THR 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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696J HIS* 5.9 4.0 - - + -
697J GLY* 3.8 1.8 - - - -
760J ARG* 3.2 29.3 + - - +
3K GLU* 4.4 8.3 - - + +
46K PRO* 4.6 15.0 - - + +
57K ASP* 3.7 13.1 + - - +
59K ASN* 3.4 20.3 + - - +
60K ALA 3.3 0.2 - - - -
61K VAL* 1.3 72.9 - - - +
63K TRP* 1.3 66.7 + - - +
65K MET* 3.2 5.2 - - + +
66K LYS* 2.9 30.1 + - + +
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Residues in contact with TRP 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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30K LEU* 3.4 18.4 - - + -
35K PHE* 3.3 59.1 - + + -
38K THR* 3.5 37.5 - - + -
40K LEU* 4.4 7.1 - - + +
45K ARG* 3.4 36.8 - - + -
46K PRO* 3.3 27.6 - - + +
56K ASP* 4.4 13.4 - - + +
57K ASP 2.9 29.2 + - - -
59K ASN 3.2 16.0 + - - -
60K ALA* 3.0 10.1 + - - +
62K THR* 1.3 79.3 - - - +
64K ALA* 1.3 57.3 + - - +
66K LYS* 3.6 1.6 + - - +
67K GLU* 2.9 33.2 + - + +
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Residues in contact with ALA 64 (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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23K VAL* 3.4 38.4 - - + +
26K ARG* 4.3 6.5 - - + -
27K ALA* 3.7 15.3 - - + +
30K LEU* 3.5 2.4 - - + +
60K ALA 2.9 8.7 + - - +
61K VAL 3.6 7.2 - - - +
63K TRP* 1.3 73.1 - - - +
65K MET* 1.3 66.2 + - - +
67K GLU* 3.0 13.3 + - - +
68K LEU* 3.0 25.5 + - - +
73K LEU* 5.0 0.3 - - - +
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Residues in contact with MET 65 (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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760J ARG* 3.3 24.0 - - - +
761J ILE* 4.2 19.1 - - + -
767J HIS* 6.3 1.3 - - - -
3K GLU* 3.9 25.4 - - + -
4K PRO 5.8 2.2 - - - +
9K LEU* 3.6 32.2 - - + +
19K LEU* 4.9 0.9 - - + -
23K VAL* 3.6 34.7 - - + +
61K VAL* 2.9 25.1 + - + +
62K THR* 3.2 12.8 - - + +
64K ALA* 1.3 78.6 - - - +
66K LYS* 1.3 63.1 + - - +
68K LEU* 3.3 7.8 + - - +
69K LEU* 3.3 21.3 + - - +
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Residues in contact with LYS 66 (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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4K PRO* 5.3 12.3 - - + +
40K LEU* 4.3 11.3 - - + +
43K GLU 5.9 0.2 + - - -
44K GLU* 4.0 28.8 + - + +
46K PRO* 5.6 7.6 - - + +
62K THR* 2.9 16.2 + - + +
63K TRP* 4.3 2.2 - - - +
65K MET* 1.3 78.1 - - - +
67K GLU* 1.3 62.3 + - - +
69K LEU* 3.4 37.8 + - + +
70K THR* 4.1 5.5 + - - +
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Residues in contact with GLU 67 (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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26K ARG* 3.2 22.0 + - - +
30K LEU* 3.2 33.9 - - - +
38K THR* 3.2 29.5 + - - +
39K VAL* 3.6 10.2 + - - +
40K LEU* 3.6 29.0 - - + +
63K TRP* 2.9 23.4 + - + +
64K ALA* 3.0 7.1 + - - +
66K LYS* 1.3 77.9 - - - +
68K LEU* 1.3 59.1 + - - +
70K THR* 2.9 25.6 + - - -
71K GLY 4.1 0.2 + - - -
73K LEU* 3.4 20.2 - - + +
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Residues in contact with LEU 68 (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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9K LEU* 3.7 24.2 - - + -
12K MET* 3.6 37.9 - - + +
13K VAL* 6.1 3.8 - - + -
19K LEU* 4.0 16.6 - - + -
22K VAL* 4.8 18.8 - - + -
23K VAL* 5.4 3.6 - - + -
64K ALA 3.0 14.0 + - - +
65K MET 3.3 4.0 + - - +
67K GLU* 1.3 71.6 - - - +
69K LEU* 1.3 56.0 + - - +
70K THR 3.0 5.2 - - - -
71K GLY* 2.8 30.0 + - - +
73K LEU* 3.6 20.2 - - + +
75K PHE* 4.6 19.1 - - + -
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Residues in contact with LEU 69 (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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4K PRO* 3.9 16.8 - - + +
5K GLY* 4.2 16.6 - - - +
8K LYS* 5.6 10.1 - - + +
9K LEU* 3.7 32.1 - - + +
12K MET* 5.5 3.9 - - - +
65K MET 3.3 18.8 - - - +
66K LYS* 3.5 42.4 - - + +
67K GLU 3.3 0.4 - - - -
68K LEU* 1.3 75.6 - - - +
70K THR* 1.3 61.9 + - + +
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Residues in contact with THR 70 (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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40K LEU* 4.2 18.2 - - + +
44K GLU* 4.3 8.7 - - + +
66K LYS 4.3 5.4 - - - +
67K GLU 2.9 18.3 + - - +
69K LEU* 1.3 80.6 - - + +
71K GLY* 1.3 60.0 + - - +
72K ARG* 3.3 52.1 + - - +
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Residues in contact with GLY 71 (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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12K MET* 5.2 8.1 - - - -
67K GLU 4.1 0.4 + - - -
68K LEU* 2.8 22.6 + - - -
70K THR* 1.3 78.6 + - - +
72K ARG* 1.3 60.9 + - - +
73K LEU 3.0 19.8 + - - +
74K PHE* 5.1 6.1 - - - -
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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