Contacts of the helix formed by residues 63 - 79 (chain K) in PDB entry 5GSE
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 ARG 63 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194I A 3.6 22.4 - - - +
195I G 3.2 29.2 + - - +
60J A 4.3 28.5 + - - +
61J A 4.5 20.2 + - - +
59K GLU* 4.3 18.6 + - - -
60K LEU 5.0 5.6 + - - -
61K LEU 4.3 0.6 + - - -
62K ILE* 1.3 73.8 + - - +
64K LYS* 1.3 79.1 + - - +
65K LEU 3.5 1.3 - - - -
66K PRO* 3.3 27.5 - - + +
67K PHE* 3.3 12.0 + - - +
29L ILE* 5.7 0.7 - - - +
30L THR* 5.9 6.6 - - + +
33L ALA* 5.2 2.0 - - - +
36L ARG* 3.6 26.1 - - - +
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Residues in contact with LYS 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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195I G 2.6 35.3 + - - +
196I C 5.6 4.9 - - - -
59K GLU* 4.7 5.7 + - - +
60K LEU* 3.5 34.9 - - + +
62K ILE 3.4 2.0 + - - -
63K ARG* 1.3 82.0 - - - +
65K LEU* 1.3 58.6 + - + +
67K PHE* 3.1 9.7 + - - +
68K GLN* 2.9 26.3 + - + +
90K MET* 3.7 31.0 - - + -
93K GLN* 3.8 10.1 + - - +
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Residues in contact with LEU 65 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194I A 3.6 27.6 - - + +
195I G 3.6 27.2 + - + +
196I C 6.0 2.2 - - + +
64K LYS* 1.3 76.4 - - + +
66K PRO* 1.3 74.0 - - + +
68K GLN* 2.8 25.2 + - + +
69K ARG* 2.9 47.2 + - - +
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Residues in contact with PRO 66 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194I A 3.6 37.2 - - - +
63K ARG* 3.3 23.1 - - + +
64K LYS 4.2 0.2 - - - +
65K LEU* 1.3 98.8 - - + +
67K PHE* 1.3 61.2 + - - +
69K ARG* 3.1 22.4 - - + +
70K LEU* 3.0 21.0 + - - +
25L ASN* 4.1 4.6 + - - +
28L GLY* 4.6 23.4 - - - +
29L ILE* 5.3 3.5 - - + +
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Residues in contact with PHE 67 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62K ILE* 3.8 18.2 - - + -
63K ARG 3.3 8.9 + - - +
64K LYS 3.1 11.3 + - - +
66K PRO* 1.3 78.8 - - - +
68K GLN* 1.3 57.1 + - - +
70K LEU* 3.0 10.5 + - + +
71K VAL* 2.9 31.3 + - + +
89K VAL* 4.0 14.1 - - + -
92K LEU* 3.9 10.8 - - + -
93K GLN* 3.4 49.4 - - + +
96K CYS* 3.6 36.8 - - + -
29L ILE* 4.1 18.3 - - + +
58L LEU* 4.8 2.5 - - + -
62L LEU* 3.7 23.6 - - + -
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Residues in contact with GLN 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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64K LYS* 2.9 16.7 + - + +
65K LEU* 2.8 22.5 + - + +
67K PHE* 1.3 75.9 - - - +
69K ARG* 1.3 57.8 + - - +
71K VAL* 2.9 25.7 - - - +
72K ARG* 3.0 46.6 + - - +
86K SER* 4.9 11.9 - - - +
89K VAL* 3.5 37.5 - - + +
90K MET* 4.7 9.8 - - + +
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Residues in contact with ARG 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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193I A 5.0 0.4 - - - -
194I A 2.3 43.8 + - - -
65K LEU* 2.9 35.3 + - - +
66K PRO* 3.1 28.2 - - - +
68K GLN* 1.3 74.7 - - - +
70K LEU* 1.3 56.3 + - - +
72K ARG* 3.7 9.5 - - - +
73K GLU* 2.9 31.9 + - - +
25L ASN* 3.2 29.5 - - - +
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Residues in contact with LEU 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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66K PRO 3.0 13.5 + - - +
67K PHE* 3.0 13.2 + - + +
69K ARG* 1.3 78.9 - - - +
71K VAL* 1.3 63.1 + - - +
73K GLU* 3.7 5.6 - - - +
74K ILE* 3.0 38.0 + - + +
25L ASN* 4.2 14.3 + - + +
26L ILE* 4.3 30.1 - - + +
29L ILE* 3.9 29.8 - - + -
58L LEU* 4.1 11.7 - - + -
59L LYS* 5.3 6.3 - - + +
62L LEU* 3.8 24.5 - - + -
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Residues in contact with VAL 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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67K PHE* 2.9 25.5 + - + +
68K GLN* 2.9 27.1 - - - +
70K LEU* 1.3 74.8 - - - +
72K ARG* 1.3 58.6 + - + +
74K ILE* 3.4 2.2 + - - +
75K ALA* 2.9 26.9 + - - +
84K PHE* 4.2 20.0 - - + -
89K VAL* 3.8 20.2 - - + -
92K LEU* 3.6 25.6 - - + -
62L LEU* 4.8 1.5 - - + +
66L ILE* 3.5 26.5 - - + +
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Residues in contact with ARG 72 (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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51J C 2.7 52.4 + - - +
52J A 5.0 12.7 + - - -
68K GLN* 3.0 47.3 + - - +
69K ARG* 3.7 7.9 - - - +
70K LEU 3.2 0.4 - - - -
71K VAL* 1.3 80.3 - - + +
73K GLU* 1.3 62.7 + - - +
75K ALA* 3.2 8.9 + - - +
76K GLN* 3.1 26.9 + - - +
82K LEU 4.2 12.5 + - - +
84K PHE* 4.1 26.8 + - + +
89K VAL* 5.4 1.2 - - + +
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Residues in contact with GLU 73 (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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69K ARG 2.9 16.3 + - - +
70K LEU* 3.7 7.6 - - - +
72K ARG* 1.3 76.0 - - - +
74K ILE* 1.3 67.8 + - + +
76K GLN* 3.0 34.0 + - - +
77K ASP* 4.1 5.7 + - - +
25L ASN* 3.0 35.6 + - + +
26L ILE 5.0 1.8 + - - -
59L LYS* 3.9 22.2 + - - -
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Residues in contact with ILE 74 (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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70K LEU* 3.0 37.5 + - + +
71K VAL 3.8 3.4 - - - +
73K GLU* 1.3 80.8 - - + +
75K ALA* 1.3 62.3 + - - +
76K GLN 3.3 0.9 + - - -
77K ASP* 3.4 17.1 + - - +
78K PHE* 3.6 17.6 - - + -
59L LYS* 4.1 31.2 - - + +
62L LEU* 3.5 30.5 - - + -
63L GLU* 4.0 26.0 - - + -
66L ILE* 3.4 19.5 - - + -
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Residues in contact with ALA 75 (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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71K VAL 2.9 18.3 + - - +
72K ARG 3.2 5.8 + - - +
74K ILE* 1.3 76.7 - - - +
76K GLN* 1.3 64.2 + - - +
77K ASP 3.1 0.9 + - - -
78K PHE* 3.1 14.7 + - - +
79K LYS 3.2 15.2 + - - +
82K LEU* 3.6 15.2 - - + +
84K PHE* 3.5 29.8 - - + -
66L ILE* 4.0 15.0 - - + -
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Residues in contact with GLN 76 (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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72K ARG* 3.1 19.0 + - - +
73K GLU* 3.0 22.9 + - - +
75K ALA* 1.3 76.9 - - - +
77K ASP* 1.3 64.4 + - - +
78K PHE 3.5 0.2 + - - -
79K LYS 3.7 17.3 + - - +
80K THR* 4.7 8.0 + - - +
81K ASP 6.2 1.1 - - - +
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Residues in contact with ASP 77 (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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73K GLU 4.1 5.5 + - - +
74K ILE* 3.8 14.2 - - - +
75K ALA 3.1 1.2 + - - -
76K GLN* 1.3 82.5 - - - +
78K PHE* 1.3 74.9 + - + +
63L GLU* 5.2 6.4 - - - +
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Residues in contact with PHE 78 (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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74K ILE* 3.6 30.7 - - + -
75K ALA* 3.1 9.7 + - - +
77K ASP* 1.3 90.5 - - + +
79K LYS* 1.3 61.9 + - - +
63L GLU* 3.4 34.8 - - + -
66L ILE* 4.5 2.9 - - + -
67L ARG* 3.1 58.1 - - + -
70L VAL* 3.6 21.5 - - + +
74L GLU* 3.7 13.2 - - - +
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Residues in contact with LYS 79 (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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75K ALA 3.2 15.3 + - - +
76K GLN* 3.7 12.7 - - - +
77K ASP 3.6 1.2 - - - -
78K PHE* 1.3 80.7 - - + +
80K THR* 1.3 79.0 + - - +
81K ASP 4.0 1.1 + - - +
82K LEU* 3.6 42.6 + - + +
70L VAL* 4.8 5.2 - - + -
73L THR* 5.5 1.0 + - - -
74L GLU* 3.7 35.1 - - + +
78L ARG 4.0 16.6 + - - -
79L LYS* 4.6 14.7 - - - +
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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