Contacts of the helix formed by residues 67 - 80 (chain L) in PDB entry 1H2I
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 GLU 67 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51L TYR 4.7 2.2 + - - -
53L SER* 3.7 13.5 + - - +
65L TYR* 3.7 27.7 + - + -
66L ILE* 1.3 77.1 - - - +
68L GLY* 1.3 62.4 + - - +
69L HIS* 3.5 28.2 - - + +
70L ARG* 2.8 50.7 + - - +
71L VAL* 3.2 7.6 + - - +
152L LYS* 4.4 0.4 - - - +
167M LEU* 5.2 3.1 - - + +
169M LYS* 4.3 26.5 + - - +
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Residues in contact with GLY 68 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66L ILE 3.5 2.8 + - - -
67L GLU* 1.3 71.5 - - - +
69L HIS* 1.3 56.6 + - - +
71L VAL* 3.1 5.2 + - - +
72L ILE* 2.9 37.6 + - - +
148L THR* 4.0 26.0 - - - +
152L LYS* 4.0 13.4 - - - +
167M LEU* 5.8 0.6 - - - +
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Residues in contact with HIS 69 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67L GLU* 3.1 36.6 + - + +
68L GLY* 1.3 75.5 - - - +
70L ARG* 1.3 79.6 + - + +
72L ILE* 4.4 0.4 - - - -
73L ASN* 3.2 20.6 + - - -
46M ARG* 5.7 1.3 - - - -
160M ASN* 6.0 0.2 - - - -
164M ASN* 3.0 51.7 - - - +
165M CYS* 5.7 0.4 - - - -
167M LEU* 3.0 35.8 - - + +
168M ASP* 3.3 48.3 + - + +
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Residues in contact with ARG 70 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50L GLU 3.9 17.1 + - - -
51L TYR* 3.8 42.0 + - + +
53L SER* 5.0 4.4 + - - -
66L ILE* 3.9 13.0 - - + -
67L GLU* 2.8 41.0 + - + +
69L HIS* 1.3 99.6 + - + +
71L VAL* 1.3 61.5 + - - +
73L ASN* 3.2 6.0 + - - +
74L LEU* 2.8 33.6 + - - +
168M ASP* 4.2 6.7 + - - -
170M ASP* 3.8 19.8 + - - -
195V ASP* 4.8 2.5 - - - +
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Residues in contact with VAL 71 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66L ILE* 3.7 29.6 - - + -
67L GLU 3.7 5.4 - - - +
68L GLY 3.1 7.3 + - - +
70L ARG* 1.3 75.1 - - - +
72L ILE* 1.3 67.0 + - + +
74L LEU* 3.2 10.9 + - + +
75L ALA* 2.9 22.9 + - - +
151L LEU* 5.5 1.8 - - + -
152L LYS* 3.9 32.1 - - + -
155L LEU* 3.8 34.8 - - + -
156L ARG* 6.1 1.3 - - - +
162L LEU* 4.3 13.4 - - + +
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Residues in contact with ILE 72 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68L GLY* 2.9 21.5 + - - +
69L HIS 3.8 0.2 - - - +
71L VAL* 1.3 77.2 - - + +
73L ASN* 1.3 58.4 + - - +
75L ALA* 3.2 8.9 + - - +
76L ASN* 2.9 32.5 + - - +
84L TRP* 4.2 9.1 - - + -
148L THR* 6.5 0.9 - - + -
151L LEU* 4.4 23.8 - - + -
156M ARG* 4.0 4.0 - - + +
157M SER* 3.4 44.6 - - - +
164M ASN* 3.5 36.1 - - + +
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Residues in contact with ASN 73 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69L HIS* 3.2 16.6 + - - +
70L ARG* 3.2 5.1 + - - +
72L ILE* 1.3 75.2 - - - +
74L LEU* 1.3 66.3 + - - +
76L ASN* 3.9 12.0 + - - +
77L GLU* 3.0 33.5 + - + +
46M ARG* 5.5 3.0 - - - +
159M GLY* 4.3 1.2 - - - -
160M ASN* 3.2 43.6 + - - +
164M ASN* 3.3 17.7 + - - +
195V ASP* 3.4 23.4 + - - +
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Residues in contact with LEU 74 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47L LEU* 3.5 25.8 - - + -
51L TYR* 3.5 36.3 - - + +
66L ILE* 5.0 5.4 - - + -
70L ARG 2.8 20.5 + - - +
71L VAL* 3.6 14.4 - - + +
73L ASN* 1.3 75.6 - - - +
75L ALA* 1.3 58.6 + - - +
77L GLU* 3.7 3.8 - - - +
78L MET* 2.8 33.8 + - + +
161L ALA 3.6 13.2 - - - +
162L LEU* 4.1 17.7 - - + +
192V LYS* 3.8 26.9 - - + +
195V ASP* 4.0 6.1 - - - +
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Residues in contact with ALA 75 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71L VAL 2.9 13.8 + - - +
72L ILE 3.4 7.9 - - - +
74L LEU* 1.3 75.3 - - - +
76L ASN* 1.3 66.2 + - - +
78L MET* 4.4 0.7 - - - -
79L PHE* 2.8 38.0 + - + +
84L TRP* 3.5 36.0 - - + -
155L LEU* 4.6 8.1 - - + -
162L LEU* 4.0 14.8 - - + +
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Residues in contact with ASN 76 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72L ILE* 2.9 29.0 + - - +
73L ASN* 4.0 7.6 + - - +
74L LEU 3.4 0.2 - - - -
75L ALA* 1.3 75.8 - - - +
77L GLU* 1.3 61.8 + - + +
80L GLY* 2.7 27.6 + - - -
81L TYR* 3.7 17.0 - - - +
84L TRP* 2.8 25.3 + - - +
40M GLN* 3.1 19.5 - - - +
121M HIS* 5.0 0.3 - - - -
157M SER 2.9 26.8 + - - +
158M PHE* 3.5 20.2 + - - +
159M GLY* 3.7 5.6 - - - +
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Residues in contact with GLU 77 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73L ASN* 3.0 23.8 + - + +
74L LEU 3.9 2.0 - - - +
76L ASN* 1.3 79.6 - - + +
78L MET* 1.3 59.9 + - - +
40M GLN* 4.1 8.6 + - - +
44M ARG* 2.5 57.1 + - - +
195V ASP* 3.5 41.1 - - + +
196V LEU* 4.1 13.2 - - - +
197V GLU* 4.4 8.2 + - - +
200V VAL* 4.1 4.9 - - - +
201V GLU* 4.5 4.7 - - - +
204V ARG* 3.1 18.9 + - - -
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Residues in contact with MET 78 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39L ILE* 3.8 15.6 - - + +
42L ALA* 3.6 33.9 - - + -
43L LEU* 3.9 25.8 - - + -
74L LEU* 2.8 20.2 + - + +
75L ALA 3.8 2.5 - - - +
77L GLU* 1.3 77.5 - - - +
79L PHE* 1.3 76.8 + - + +
161L ALA* 3.8 28.3 - - + +
162L LEU* 4.1 9.0 - - + -
192V LYS* 4.4 5.2 - - - -
197V GLU* 4.1 21.5 - - + +
200V VAL* 3.4 16.1 - - - +
204V ARG* 3.4 12.6 + - - -
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Residues in contact with PHE 79 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31L TYR* 3.8 18.5 + - - +
35L GLU* 4.5 2.1 - - - +
39L ILE* 4.2 20.2 - - + -
43L LEU* 4.6 3.6 - - + -
75L ALA* 2.8 26.4 + - + +
78L MET* 1.3 94.2 - - + +
80L GLY* 1.3 59.4 + - - +
82L ASN* 4.4 1.0 + - - -
83L GLY* 3.2 32.8 - - - -
84L TRP* 3.9 20.0 - + + -
115L LEU* 4.1 23.3 - - + -
116L LYS* 4.8 3.5 + - - -
155L LEU* 5.0 2.0 - - + -
158L PHE* 4.0 34.8 - + + -
162L LEU* 4.6 11.4 - - + -
81V TYR* 4.4 4.7 - + - -
204V ARG* 3.4 19.5 + - - +
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Residues in contact with GLY 80 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76L ASN 2.7 22.6 + - - -
79L PHE* 1.3 74.2 - - - +
81L TYR* 1.3 64.2 + - - -
82L ASN* 2.9 12.3 - - - -
83L GLY 2.9 11.1 + - - -
84L TRP* 3.5 12.0 - - - -
36M TYR* 3.9 3.8 - - - -
40M GLN* 3.5 9.4 - - - -
204V ARG* 3.5 16.0 - - - +
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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