Contacts of the helix formed by residues 61 - 75 (chain A) in PDB entry 5UC7
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 HIS 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A HIS* 3.6 35.2 + - + +
58A GLY 5.2 0.9 - - - +
59A TYR 3.1 4.6 + - - +
60A ASN* 1.3 74.7 - - - +
62A PRO* 1.3 77.7 - - + +
63A GLN* 3.1 45.3 + - + +
64A LEU* 3.1 23.9 + - + +
65A ASN* 2.9 25.6 + - - -
326A LEU* 3.5 32.2 - - + +
404A ILE* 5.3 8.4 - - + +
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Residues in contact with PRO 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ASN 3.5 7.2 - - - +
61A HIS* 1.3 91.9 - - + +
63A GLN* 1.3 76.1 + - - +
65A ASN* 3.8 8.7 - - + +
66A ALA* 3.0 29.5 + - - +
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Residues in contact with GLN 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A HIS* 3.1 27.2 + - + +
62A PRO* 1.3 91.4 + - - +
64A LEU* 1.4 64.7 + - - +
66A ALA* 3.6 5.6 + - - +
67A ALA* 3.1 24.3 + - - +
322A ALA* 4.0 7.4 - - + +
326A LEU* 4.3 19.3 - - + +
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Residues in contact with LEU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A HIS* 4.1 21.1 - - + -
58A GLY 5.3 3.6 - - - +
61A HIS* 3.1 26.5 + - + +
63A GLN* 1.4 73.8 - - - +
65A ASN* 1.3 68.9 + - - +
67A ALA* 3.3 2.8 + - - +
68A MET* 3.0 30.0 + - - +
278A GLY* 4.4 10.1 - - - +
280A THR* 4.1 22.4 - - + -
319A VAL* 3.9 16.1 - - + +
322A ALA* 3.7 10.5 - - + -
323A SER* 3.4 40.2 - - - +
326A LEU* 4.0 10.1 - - + -
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Residues in contact with ASN 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ASN* 2.8 42.7 + - - -
61A HIS 2.9 22.1 + - - +
62A PRO* 3.8 7.8 - - + +
64A LEU* 1.3 77.6 - - - +
66A ALA* 1.3 63.6 + - - +
68A MET* 3.3 13.6 + - - +
69A LYS* 3.0 39.8 + - - +
280A THR* 6.1 0.7 - - - +
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Residues in contact with ALA 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A PRO 3.0 19.1 + - - +
63A GLN* 4.0 6.7 - - - +
65A ASN* 1.3 76.7 - - - +
67A ALA* 1.3 57.4 + - - +
69A LYS* 3.4 6.4 + - - +
70A THR* 2.9 37.1 + - - +
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Residues in contact with ALA 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLN 3.1 18.6 + - - +
64A LEU 3.8 2.9 - - - +
65A ASN 3.3 0.2 - - - -
66A ALA* 1.3 77.0 - - - +
68A MET* 1.3 63.8 + - - +
70A THR* 3.5 5.4 + - - -
71A GLN* 3.1 23.0 + - - +
318A ALA* 4.0 17.8 - - + +
319A VAL* 4.7 0.9 - - - -
322A ALA* 3.5 24.5 - - + -
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Residues in contact with MET 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A LEU 3.0 20.7 + - - +
65A ASN* 3.6 14.6 - - - +
67A ALA* 1.3 75.6 - - - +
69A LYS* 1.3 59.6 + - + +
71A GLN 3.2 1.0 + - - -
72A ILE* 2.9 38.9 + - + +
280A THR* 3.8 31.0 - - - +
281A MET* 3.6 31.2 - - + -
315A LEU* 3.6 23.5 - - + +
319A VAL* 3.7 22.4 - - + +
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Residues in contact with LYS 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ASN* 3.0 33.2 + - + +
66A ALA* 4.1 4.9 - - - +
68A MET* 1.3 77.2 - - + +
70A THR* 1.3 64.2 + - - +
72A ILE* 3.4 15.2 + - + +
73A ASP* 3.1 30.2 + - - +
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Residues in contact with THR 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ALA* 2.9 21.0 + - - +
67A ALA* 3.8 6.3 - - - -
69A LYS* 1.3 78.6 - - - +
71A GLN* 1.3 62.7 + - - +
73A ASP* 3.3 18.1 + - - +
74A ALA* 3.4 11.1 + - - +
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Residues in contact with GLN 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ALA 3.1 11.9 + - - +
68A MET 3.9 3.1 - - - +
70A THR* 1.3 75.7 - - - +
72A ILE* 1.3 66.0 + - - +
74A ALA* 3.0 14.6 + - - +
75A MET* 2.9 59.8 + - - +
76A SER* 5.0 0.2 - - - -
87A PRO* 3.3 26.9 - - - +
314A PRO* 3.6 32.2 - - - +
315A LEU* 3.9 8.5 - - + -
318A ALA* 3.6 19.5 - - + +
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Residues in contact with ILE 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A MET* 2.9 29.2 + - + +
69A LYS* 3.7 14.8 - - + +
70A THR 3.3 0.2 - - - -
71A GLN* 1.3 76.9 - - - +
73A ASP* 1.3 66.1 + - - +
74A ALA 3.3 1.2 + - - -
75A MET* 3.6 9.0 + - - -
76A SER* 3.7 26.1 + - - +
315A LEU* 4.0 20.9 - - + -
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Residues in contact with ASP 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A LYS* 3.1 19.2 + - - +
70A THR* 3.5 12.2 - - + +
71A GLN 3.2 0.4 - - - -
72A ILE* 1.3 80.9 - - - +
74A ALA* 1.3 61.3 + - - +
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Residues in contact with ALA 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A THR 3.4 8.2 + - - +
71A GLN* 3.0 22.2 + - - +
72A ILE 4.0 0.4 - - - -
73A ASP* 1.3 83.0 - - - +
75A MET* 1.3 65.8 + - + +
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Residues in contact with MET 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLN* 2.9 43.0 + - - +
72A ILE 3.6 3.8 + - - -
74A ALA* 1.3 77.8 - - + +
76A SER* 1.3 64.1 + - - +
77A HIS 4.5 8.5 - - - +
78A VAL* 3.7 31.9 - - + -
85A HIS* 3.7 29.8 - - + -
87A PRO* 5.6 0.7 - - + -
314A PRO* 3.7 12.0 - - + +
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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