Contacts of the helix formed by residues 74 - 86 (chain I) in PDB entry 6K71
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 ALA 74 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67I LEU* 4.0 21.8 - - + +
68I LEU 3.3 15.0 - - - +
69I PRO* 4.4 0.2 - - - -
73I VAL* 1.3 74.9 - - - +
75I LEU* 1.3 65.5 + - - +
76I ILE 3.6 2.7 - - - +
77I ASP* 3.1 29.7 + - - +
78I TYR* 3.1 17.1 - - - -
105I HIS* 3.7 25.2 + - + +
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Residues in contact with LEU 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65I ARG* 4.2 20.0 - - + +
66I VAL* 3.4 15.0 + - - +
68I LEU* 3.2 31.4 - - + +
70I LEU* 4.4 17.7 - - + +
74I ALA* 1.3 75.4 - - - +
76I ILE* 1.3 61.1 + - - +
77I ASP 3.1 2.2 - - - -
78I TYR* 2.8 24.3 + - + +
79I THR* 2.9 17.5 + - + +
153I GLY 4.1 8.1 - - - +
154I ASP* 3.7 21.8 - - + +
156I ILE* 4.5 13.2 - - + -
300I VAL* 3.7 28.5 - - + -
306I TYR* 5.8 3.6 - - + -
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Residues in contact with ILE 76 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47I LEU* 4.0 15.7 - - + -
49I ALA* 4.8 1.8 - - + -
66I VAL* 3.7 29.4 + - + +
67I LEU* 3.6 26.9 - - + -
74I ALA* 3.6 1.2 - - - +
75I LEU* 1.3 72.7 - - - +
77I ASP* 1.3 65.1 + - - +
79I THR* 3.0 20.1 + - - +
80I LEU* 3.0 29.8 + - + -
93I VAL* 5.5 1.6 - - + -
102I ILE* 3.7 25.4 - - + +
105I HIS* 5.6 6.5 - - + -
106I LEU* 4.3 20.6 - - + +
111I TRP* 3.7 6.9 - - - -
153I GLY 5.0 1.6 - - - +
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Residues in contact with ASP 77 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73I VAL* 4.0 4.1 - - + +
74I ALA 3.1 32.0 + - - +
76I ILE* 1.3 76.0 - - - +
78I TYR* 1.3 51.6 + - + +
81I GLU* 2.6 47.5 + - - +
105I HIS* 3.1 28.5 + - - +
109I SER* 4.8 7.8 - - - -
111I TRP* 3.3 19.3 - - + -
328I THR* 3.7 30.2 - - + +
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Residues in contact with TYR 78 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70I LEU* 3.3 46.9 - - + +
71I ALA* 3.6 8.8 + - - +
73I VAL* 3.2 28.4 - - + +
74I ALA 3.1 25.4 - - - -
75I LEU* 2.8 19.0 + - + +
77I ASP* 1.3 73.4 - - + +
79I THR* 1.3 59.3 + - - +
81I GLU* 3.5 12.4 - - - +
82I PHE* 2.8 31.9 + - - +
155I VAL 3.9 13.7 - - - +
156I ILE* 4.1 26.0 - - + -
157I SER 5.0 0.3 + - - +
313I VAL* 5.0 7.4 - - + +
318I VAL* 6.3 0.4 - - + -
321I LEU* 3.7 28.1 - - + +
322I THR 5.8 1.8 - - - -
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Residues in contact with THR 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47I LEU* 4.0 13.9 - - - +
75I LEU 2.9 10.1 + - - +
76I ILE* 3.0 17.2 + - - +
78I TYR* 1.3 75.6 - - - +
80I LEU* 1.3 75.2 + - - +
82I PHE* 3.3 9.7 - - - +
83I LEU* 2.9 29.5 + - - +
151I VAL* 4.6 3.5 - - - +
153I GLY* 3.3 34.3 - - - +
155I VAL* 3.4 30.1 - - + +
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Residues in contact with LEU 80 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47I LEU* 3.7 27.6 - - + -
76I ILE* 3.0 14.9 + - + -
79I THR* 1.3 93.5 + - - +
81I GLU* 1.3 59.9 + - - +
83I LEU* 3.5 15.3 - - + -
84I THR* 2.8 31.9 + - - +
91I THR* 4.0 17.0 - - + -
93I VAL* 4.2 10.3 - - + -
106I LEU* 4.7 1.8 - - + -
111I TRP* 3.4 44.8 - - + +
118I ASN* 4.1 4.9 + - - +
120I VAL* 3.8 20.0 - - + -
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Residues in contact with GLU 81 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73I VAL* 6.1 0.3 - - - +
77I ASP* 2.6 38.6 + - - +
78I TYR* 3.5 15.7 + - - +
80I LEU* 1.3 75.1 - - - +
82I PHE* 1.3 59.6 + - - +
84I THR* 3.3 9.5 - - - +
85I ALA* 2.9 30.3 + - - +
111I TRP* 3.9 7.5 - - + -
321I LEU* 4.0 25.0 - - + +
325I ALA* 3.3 16.8 - - - +
327I PHE* 3.1 51.8 - - + +
328I THR* 5.5 2.3 - - - +
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Residues in contact with PHE 82 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78I TYR 2.8 21.5 + - - +
79I THR* 3.3 8.3 - - - +
81I GLU* 1.3 70.9 - - - +
83I LEU* 1.3 65.3 + - + +
85I ALA* 3.1 8.2 + - + +
86I THR* 3.0 30.2 + - + +
149I LEU* 6.1 1.1 - - + -
151I VAL* 5.1 7.2 - - + -
155I VAL* 4.9 11.2 - - + -
157I SER* 3.2 43.5 - - - +
158I ASN* 3.7 5.2 - - - -
159I ILE* 3.1 44.6 - - + -
161I ILE* 4.0 17.9 - - + -
249I ILE* 4.4 24.9 - - + -
321I LEU* 3.9 7.8 - - + +
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Residues in contact with LEU 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45I ALA* 3.7 18.4 - - + -
47I LEU* 5.8 6.7 - - + +
79I THR 2.9 18.7 + - - +
80I LEU* 3.8 13.5 - - + -
81I GLU 3.2 0.4 - - - -
82I PHE* 1.3 79.9 - - + +
84I THR* 1.3 62.4 + - - +
86I THR* 3.3 14.9 - - + +
88I VAL* 3.3 47.6 + - + +
91I THR* 3.6 29.6 - - + -
118I ASN* 3.9 9.9 - - - +
149I LEU* 4.4 4.3 - - + -
151I VAL* 4.1 26.9 - - + -
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Residues in contact with THR 84 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C GLU* 4.3 15.0 - - + +
80I LEU 2.8 20.7 + - - +
81I GLU* 3.3 11.4 - - - +
83I LEU* 1.3 75.8 - - - +
85I ALA* 1.3 67.2 + - - +
87I GLY* 3.6 8.8 + - - -
88I VAL 4.4 8.2 + - - +
111I TRP* 4.8 15.2 - - + +
116I SER* 5.2 5.2 - - - -
117I LEU 5.6 0.2 + - - -
118I ASN* 3.8 28.9 + - - +
327I PHE* 5.7 9.4 - - + -
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Residues in contact with ALA 85 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C GLU* 4.6 8.9 - - - +
24C ARG* 4.2 28.4 + - + +
81I GLU 2.9 19.1 + - - +
82I PHE* 3.1 11.2 + - + +
84I THR* 1.3 80.3 - - - +
86I THR* 1.3 60.6 + - - +
87I GLY* 3.4 1.0 + - - -
321I LEU* 4.9 10.5 - - + -
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Residues in contact with THR 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82I PHE* 3.0 16.8 + - + +
83I LEU* 3.3 20.0 - - + +
85I ALA* 1.3 76.1 - - - +
87I GLY* 1.3 59.2 + - - +
88I VAL* 3.7 15.4 - - + +
149I LEU* 6.5 0.4 - - + -
159I ILE 4.6 5.6 - - - -
160I ASN* 3.7 11.3 + - - +
161I ILE* 3.3 46.8 + - + +
162I THR* 4.2 9.5 + - - +
165I LEU* 5.8 0.9 - - - +
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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