Contacts of the helix formed by residues 60 - 74 (chain A) in PDB entry 6XWQ
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 VAL 60 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LEU 4.5 0.4 - - - +
57A LYS* 3.3 16.2 - - + +
58A MET 3.4 0.8 - - - -
59A LEU* 1.3 79.9 - - - +
61A MET* 1.3 77.9 + - + +
64A VAL* 3.2 28.0 + - - +
153A VAL* 4.9 5.6 - - + +
281A SER* 3.5 19.6 + - - +
311A THR* 5.2 4.0 - - + -
356A ALA* 4.0 12.3 - - + -
357A GLY 3.6 26.5 - - - +
358A VAL* 3.7 22.0 - - + -
143C ASN* 5.6 3.4 - - - +
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Residues in contact with MET 61 (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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58A MET 4.6 0.2 + - - -
60A VAL* 1.3 86.4 - - + +
62A PRO* 1.3 69.3 - - + +
63A ILE 3.3 0.2 - - - -
64A VAL* 3.1 9.5 - - - +
65A LEU* 3.0 25.5 + - - +
147A SER 4.7 0.7 - - - +
148A LEU* 3.8 24.5 - - + +
151A GLY* 3.3 35.2 - - - +
152A GLU 3.4 9.6 - - - +
153A VAL* 3.8 16.4 - - + -
156A VAL* 3.6 34.3 - - - -
143C ASN* 3.3 25.5 + - - +
145C PHE* 3.8 9.4 - - + -
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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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58A MET 3.4 18.6 - - - +
59A LEU 4.5 0.7 - - - -
60A VAL 4.0 1.3 - - - +
61A MET* 1.3 94.1 - - + +
63A ILE* 1.3 63.1 + - - +
65A LEU* 3.9 2.9 - - + +
66A ALA* 2.9 29.6 + - - +
192A LEU* 5.1 8.0 - - + +
196A MET* 3.6 32.3 - - + -
144C PRO* 3.7 27.1 - - + -
145C PHE* 4.2 20.9 - - + -
159C PHE* 4.7 1.8 - - + -
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Residues in contact with ILE 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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59A LEU* 3.1 33.2 - - + +
60A VAL 4.4 0.2 + - - -
61A MET 3.3 0.6 - - - -
62A PRO* 1.3 76.3 - - - +
64A VAL* 1.3 65.9 + - - +
66A ALA* 5.1 1.3 - - - -
67A SER* 2.8 32.7 + - - -
193A ALA* 5.9 1.6 - - - +
196A MET* 3.5 29.8 - - + +
197A TYR* 4.2 16.2 - - + -
200A VAL* 3.4 32.3 - - + -
281A SER* 4.1 11.7 - - - +
284A LEU* 3.7 31.6 - - + -
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Residues in contact with VAL 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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60A VAL 3.2 17.7 + - - +
61A MET* 3.1 30.0 + - - +
63A ILE* 1.3 79.0 - - - +
65A LEU* 1.3 67.0 + - - +
67A SER* 5.0 0.4 - - - -
68A LEU* 2.9 43.6 + - + +
153A VAL* 4.8 6.7 - - + -
156A VAL* 4.1 9.2 - - + -
157A ILE* 3.6 30.1 - - + -
160A ALA* 5.3 0.2 - - - -
281A SER* 5.5 0.9 + - - +
284A LEU* 6.2 1.1 - - - -
307A PRO 4.7 1.1 - - - +
311A THR* 3.7 27.1 - - + +
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Residues in contact with LEU 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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61A MET 3.0 17.3 + - - +
62A PRO* 3.9 2.9 - - + +
64A VAL* 1.3 79.6 - - - +
66A ALA* 1.3 66.4 + - - +
69A VAL* 3.0 34.8 + - + +
148A LEU* 4.0 23.8 - - + -
156A VAL* 3.9 19.5 - - + -
159A PHE* 4.7 15.7 - - + -
160A ALA* 3.6 22.0 - - + +
163A LEU* 5.9 0.4 - - + -
189A PHE* 4.7 21.8 - - + -
192A LEU* 5.5 4.9 - - + -
145C PHE* 4.2 16.4 - - + -
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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 2.9 19.8 + - - +
63A ILE* 4.4 0.7 - - - +
65A LEU* 1.3 76.8 - - - +
67A SER* 1.3 59.1 + - - +
69A VAL* 3.2 4.4 + - - +
70A VAL* 2.9 32.7 + - - +
189A PHE* 3.7 28.9 - - + +
192A LEU* 3.9 20.2 - - + -
193A ALA* 3.9 17.3 - - + +
196A MET* 5.9 0.2 - - + -
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Residues in contact with SER 67 (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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63A ILE* 2.8 29.7 + - - -
64A VAL* 4.5 0.4 - - - -
66A ALA* 1.3 71.1 - - - +
68A LEU* 1.3 61.3 + - - +
70A VAL* 3.4 3.6 + - - +
71A GLY* 2.9 27.4 + - - -
193A ALA* 4.2 13.2 - - - +
197A TYR* 3.2 24.3 + - - -
284A LEU* 5.2 0.8 - - - +
303A SER* 4.0 4.2 + - - +
307A PRO* 3.0 28.9 - - - +
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Residues in contact with LEU 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 VAL* 2.9 43.9 + - + +
67A SER* 1.3 73.6 - - - +
69A VAL* 1.3 67.9 + - - +
71A GLY* 5.1 0.7 - - - -
72A ALA* 2.9 29.2 + - - +
157A ILE* 4.6 15.7 - - + +
160A ALA* 3.9 18.8 - - + -
161A ILE* 5.0 6.1 - - + -
304A PHE* 3.8 33.2 - - + +
307A PRO* 3.5 33.2 - - + +
308A LEU* 4.1 20.4 - - + +
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Residues in contact with VAL 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 LEU* 3.0 21.7 + - + +
66A ALA 3.5 7.2 - - - +
68A LEU* 1.3 76.3 - - - +
70A VAL* 1.3 60.3 + - + +
72A ALA 3.7 0.7 - - - -
73A ALA* 2.9 29.6 + - - +
160A ALA* 3.3 33.7 - - + +
163A LEU* 4.2 9.2 - - + -
164A GLY* 3.8 4.4 - - - -
167A ILE* 4.3 17.9 - - + -
186A LEU* 4.9 3.8 - - + -
189A PHE* 3.3 44.2 - - + -
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Residues in contact with VAL 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 20.5 + - - +
67A SER* 3.9 5.6 - - - +
69A VAL* 1.3 75.7 - - - +
71A GLY* 1.3 59.8 + - - +
73A ALA* 3.3 0.9 + - - +
74A SER* 2.9 39.5 + - - +
186A LEU* 4.2 14.7 - - + +
189A PHE* 3.6 10.3 - - + +
190A ASP* 3.5 52.7 - - + +
193A ALA* 4.7 4.3 - - + -
303A SER* 4.8 8.1 - - - +
177C ARG* 6.0 0.9 - - - +
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Residues in contact with GLY 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 SER 2.9 13.3 + - - -
68A LEU 3.9 0.4 - - - -
70A VAL* 1.3 80.8 - - - +
72A ALA* 1.3 59.5 + - - +
73A ALA 3.3 0.7 + - - -
74A SER* 3.4 4.2 + - - -
75A ILE* 3.1 26.7 - - - +
303A SER* 3.3 34.9 + - - -
304A PHE* 4.2 9.2 - - - -
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Residues in contact with ALA 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 LEU 2.9 17.5 + - - +
69A VAL 3.7 1.8 - - - +
71A GLY* 1.3 75.5 - - - +
73A ALA* 1.3 57.4 + - - +
74A SER 3.6 0.2 - - - -
75A ILE 4.1 6.1 - - - +
80A LEU* 3.2 34.3 - - + +
161A ILE* 3.7 42.0 - - + +
164A GLY* 3.6 11.3 - - - +
168A THR* 4.3 2.1 - - - +
304A PHE* 4.5 5.6 - - + -
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Residues in contact with ALA 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 VAL* 2.9 18.7 + - + +
72A ALA* 1.3 76.9 - - - +
74A SER* 1.3 56.7 + - - +
75A ILE 3.2 5.4 - - - -
164A GLY* 3.4 21.5 - - - +
167A ILE* 4.0 13.9 - - + -
168A THR* 3.3 20.2 + - - +
171A MET* 4.2 13.9 - - - +
186A LEU* 3.6 25.2 - - + +
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Residues in contact with SER 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 VAL* 2.9 26.7 + - - +
71A GLY* 3.4 6.1 + - - -
73A ALA* 1.3 76.7 - - - +
75A ILE* 1.3 61.8 + - - +
76A SER 4.5 0.2 + - - -
79A ARG* 5.1 5.7 + - - -
171A MET* 6.1 0.2 - - - -
186A LEU* 5.0 8.6 - - - +
300A GLY* 5.3 4.1 - - - -
303A SER* 5.5 4.9 - - - -
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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