Contacts of the helix formed by residues 67 - 78 (chain C) in PDB entry 5IWM
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 SER 67 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65C LYS 3.5 2.2 + - - -
66C LYS* 1.3 71.8 - - - +
68C ALA* 1.3 57.0 + - - +
70C ILE* 3.3 11.2 + - - +
71C VAL* 2.8 36.8 + - - +
87C TYR* 3.8 15.3 - - - -
90C MET* 3.6 15.4 - - - +
110C PHE* 4.5 0.3 - - - -
121C MET* 3.4 7.4 - - - -
124C THR* 2.8 44.6 + - - -
125C GLU* 3.6 7.6 + - - -
126C ALA 4.3 0.2 + - - -
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Residues in contact with ALA 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A GLY* 4.7 10.0 - - - +
75A MET* 3.9 31.0 - - + -
76A GLY* 6.0 0.9 - - - +
66C LYS* 4.8 6.7 - - + -
67C SER* 1.3 79.7 - - - +
69C ARG* 1.3 56.3 + - + +
71C VAL* 3.9 0.3 - - - -
72C GLY* 2.9 27.5 + - - -
121C MET* 3.6 23.3 + - + +
122C ARG* 4.6 5.4 - - - +
101F 6EJ 3.5 15.0 - - - +
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Residues in contact with ARG 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLN* 6.0 0.2 - - - +
72A GLY* 3.2 26.9 - - - +
73A ASP* 2.9 35.6 + - - +
76A GLY* 4.6 11.9 - - - -
77A LYS* 3.5 33.5 - - - +
154A GLU* 5.5 1.6 + - - -
56C GLN* 5.6 3.2 + - - -
58C MET* 5.4 7.0 - - + -
65C LYS* 6.2 0.4 - - + -
66C LYS* 3.1 26.0 + - + +
68C ALA* 1.3 73.4 - - + +
70C ILE* 1.3 66.3 + - + +
72C GLY* 3.3 1.0 + - - -
73C ASP* 2.9 40.3 + - - +
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Residues in contact with ILE 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ILE* 4.9 6.1 - - + +
52C GLY 5.8 1.1 - - - -
53C LEU* 3.9 30.3 - - + +
58C MET* 3.5 26.7 - - + +
65C LYS 4.2 0.9 - - - +
66C LYS 3.1 18.6 + - - +
67C SER* 3.5 15.3 - - - +
69C ARG* 1.3 77.4 - - - +
71C VAL* 1.3 64.3 + - + +
73C ASP* 3.8 3.2 - - - +
74C VAL* 3.0 39.6 + - + +
86C ILE* 6.4 0.4 - - + -
90C MET* 4.0 18.6 - - - -
126C ALA* 4.0 27.8 - - + +
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Residues in contact with VAL 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C SER 2.8 24.4 + - - +
70C ILE* 1.3 76.7 - - + +
72C GLY* 1.3 62.0 + - - +
74C VAL* 3.9 0.9 - - - +
75C MET* 3.0 40.4 + - + +
83C ASP* 3.8 21.3 - - + +
86C ILE* 4.1 19.0 - - + +
87C TYR* 3.9 36.1 - - + +
90C MET* 4.8 8.5 - - + -
121C MET* 3.9 17.5 - - + -
101F 6EJ 4.8 0.4 - - - -
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Residues in contact with GLY 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ALA* 4.7 10.0 - - - +
69A ARG* 3.3 21.8 + - - +
72A GLY* 6.1 0.4 - - - -
68C ALA 2.9 19.4 + - - -
69C ARG* 3.7 1.8 - - - -
70C ILE 3.2 0.2 - - - -
71C VAL* 1.3 77.4 - - - +
73C ASP* 1.3 61.7 + - - +
75C MET* 4.1 6.5 - - - +
76C GLY* 3.4 11.8 + - - -
101F 6EJ 3.9 16.3 - - - -
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Residues in contact with ASP 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ARG* 2.9 39.0 + - - +
73A ASP* 4.7 10.4 - - - +
52C GLY* 6.3 2.2 - - - -
56C GLN* 4.2 27.2 - - + +
58C MET* 6.0 0.9 - - - +
69C ARG* 2.9 28.8 + - - +
70C ILE* 3.8 3.8 - - - +
72C GLY* 1.3 74.6 - - - +
74C VAL* 1.3 68.0 + - + +
76C GLY 3.4 0.5 + - - -
77C LYS* 3.0 38.2 + - + +
78C TYR* 5.1 1.1 - - + -
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Residues in contact with VAL 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C VAL 5.3 0.2 - - - +
48C ARG* 3.8 36.6 - - + +
49C ILE* 4.0 15.7 - - + +
52C GLY* 4.5 12.1 - - - -
70C ILE* 3.0 27.4 + - + +
71C VAL* 3.9 3.4 - - - +
73C ASP* 1.3 76.4 - - + +
75C MET* 1.3 51.7 + - - +
78C TYR* 2.9 20.5 + - + -
79C HIS* 2.7 45.9 + - + -
86C ILE* 4.1 18.2 - - + -
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Residues in contact with MET 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ALA* 4.4 6.1 - - + -
121A MET* 6.5 0.2 - - - -
122A ARG* 3.7 29.4 - - + -
71C VAL* 3.0 21.8 + - + +
72C GLY* 4.1 4.3 - - - +
74C VAL* 1.3 77.2 - - - +
76C GLY* 1.3 62.4 + - - +
79C HIS 2.7 30.9 + - - +
80C PRO* 3.9 2.5 - - - +
81C HIS 3.2 27.6 - - - +
83C ASP* 3.2 35.0 - - + -
86C ILE* 3.6 9.4 - - + -
150C TYR* 3.9 6.2 + - - -
581D LYS* 5.8 0.9 - - - +
101F 6EJ 3.5 25.4 - - - -
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Residues in contact with GLY 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A LYS* 4.4 27.4 + - - +
68A ALA* 6.5 0.7 - - - -
69A ARG* 4.4 7.6 - - - -
72C GLY 3.4 9.7 + - - -
73C ASP 3.4 4.1 + - - -
74C VAL 3.3 0.4 - - - -
75C MET* 1.3 81.3 - - - +
77C LYS* 1.3 59.9 + - - +
149C ASN* 5.0 1.2 + - - -
150C TYR* 2.7 25.6 + - - -
151C ASP* 5.0 1.4 - - - +
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Residues in contact with LYS 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ARG* 3.9 38.0 - - - +
55C GLU* 6.0 1.0 - - - +
56C GLN* 3.6 24.8 - - - +
73C ASP* 3.0 23.2 + - + +
76C GLY* 1.3 79.0 - - - +
78C TYR* 1.3 97.9 + - + +
149C ASN* 2.9 27.0 + - - -
150C TYR* 3.8 1.7 - - - -
154C GLU* 3.8 33.4 - - + +
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Residues in contact with TYR 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C ARG* 3.2 45.8 + - + -
51C TYR* 3.5 38.1 + + - -
52C GLY* 4.5 14.1 - - - -
55C GLU* 4.3 12.6 - - - +
56C GLN* 5.9 0.2 + - - -
73C ASP 5.2 0.4 - - - -
74C VAL* 2.9 26.1 + - - -
76C GLY 3.7 0.2 - - - -
77C LYS* 1.3 114.1 + - + +
79C HIS* 1.3 57.9 + - - +
80C PRO* 3.1 13.9 - - - +
149C ASN* 4.8 3.8 - - + -
150C TYR* 3.7 11.8 + - - +
154C GLU* 4.4 10.6 + - + -
155C ARG 3.7 10.9 + - - -
156C GLU* 3.9 22.9 - - + +
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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