Contacts of the helix formed by residues 43 - 56 (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 LYS 43 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ARG 3.5 20.4 - - - +
34C ALA* 3.3 18.3 + - - +
35C LEU 4.0 17.9 - - - +
36C PRO* 4.2 4.5 - - + -
42C LEU* 1.3 78.1 - - - +
44C PRO* 1.4 75.5 - - + +
45C VAL* 3.3 6.2 + - + +
46C HIS* 3.3 34.8 + - + +
47C ARG* 3.1 23.0 + - - +
172C ALA* 4.8 13.7 - - - -
173C SER 2.4 34.9 + - - +
174C GLY* 3.7 3.6 - - - -
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Residues in contact with PRO 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C VAL 4.8 0.9 - - - +
32C ALA* 3.3 33.4 - - + +
33C ARG* 3.6 20.9 - - - +
35C LEU 4.7 4.9 - - - +
43C LYS* 1.4 84.5 - - + +
45C VAL* 1.3 61.6 + - - +
47C ARG* 3.5 2.4 + - - +
48C ARG* 3.1 46.1 + - - +
79C HIS* 4.8 3.4 - - + -
501C GOL 3.5 39.2 + - - +
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Residues in contact with VAL 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ARG 5.7 1.6 - - - +
43C LYS* 4.7 6.3 - - + -
44C PRO* 1.3 79.4 - - - +
46C HIS* 1.3 86.4 + - + +
48C ARG* 3.5 2.2 + - - +
49C ILE* 3.0 38.1 + - + +
79C HIS* 3.5 41.8 - - + +
85C SER* 4.7 3.8 - - - +
86C ILE* 4.2 22.2 - - + +
89C ALA* 4.0 12.1 - - + -
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Residues in contact with HIS 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C LEU* 3.8 20.9 - - + -
43C LYS* 3.3 41.3 + - + +
45C VAL* 1.3 92.8 - - + +
47C ARG* 1.3 61.3 + - - +
49C ILE* 3.4 6.4 + - - +
50C LEU* 3.2 31.0 + - - +
89C ALA* 3.8 25.7 + - + +
92C ARG* 4.8 10.3 + - - +
93C MET* 3.6 30.9 - - + +
99C TYR* 3.7 15.5 + - - -
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Residues in contact with ARG 47 (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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37C ASP* 3.7 13.3 + - - +
40C ASP* 2.7 32.4 + - - -
42C LEU* 3.1 38.0 + - + +
43C LYS 3.1 9.0 + - - +
44C PRO* 3.9 9.0 - - - +
46C HIS* 1.3 75.1 - - - +
48C ARG* 1.3 57.7 + - + +
50C LEU* 4.1 3.1 - - - +
51C TYR* 3.1 29.1 + - - +
157C PRO* 3.8 23.8 - - + -
158C SER 3.7 10.3 + - - -
159C VAL* 3.7 11.2 - - - +
160C LEU* 3.6 23.5 - - + +
501C GOL 2.9 44.8 + - - +
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Residues in contact with ARG 48 (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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32C ALA* 5.9 2.4 - - - +
44C PRO* 3.1 27.2 + - - +
45C VAL* 3.8 5.2 - - - +
46C HIS 3.3 0.2 - - - -
47C ARG* 1.3 75.6 - - + +
49C ILE* 1.3 58.4 + - - +
51C TYR* 4.0 4.3 - - - +
52C GLY* 3.1 23.7 + - - -
74C VAL* 3.8 22.1 - - + +
78C TYR* 3.2 39.8 + - + -
79C HIS* 3.0 33.5 + - - -
80C PRO* 3.8 10.3 - - - +
81C HIS* 4.8 3.0 + - - -
150C TYR* 6.1 2.0 - - - +
156C GLU* 3.1 31.1 + - + +
157C PRO* 6.5 0.2 - - - -
501C GOL 3.1 34.2 + - - +
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Residues in contact with ILE 49 (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* 3.0 21.0 + - + +
46C HIS 3.7 4.5 - - - +
48C ARG* 1.3 77.6 - - - +
50C LEU* 1.3 62.4 + - - +
52C GLY* 3.4 1.7 + - - -
53C LEU* 3.2 31.6 + - + +
70C ILE* 4.9 6.2 - - + +
74C VAL* 4.0 11.4 - - + +
86C ILE* 3.5 42.8 - - + +
89C ALA* 3.9 10.1 - - + -
90C MET* 3.7 35.4 - - + +
93C MET* 3.6 22.7 - - + -
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Residues in contact with LEU 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C LEU* 4.2 17.0 - - + -
46C HIS 3.2 17.8 + - - +
47C ARG 4.1 3.1 - - - +
49C ILE* 1.3 73.0 - - - +
51C TYR* 1.3 65.4 + - - +
53C LEU* 3.3 23.1 + - + +
54C ASN* 3.1 21.5 + - - +
93C MET* 4.1 21.5 - - + -
103C LEU* 4.2 22.7 - - + +
104C VAL* 4.4 0.4 - - + -
132C THR* 4.0 21.1 - - + -
135C LEU* 4.0 26.7 - - + -
136C LEU* 3.7 9.2 - - + +
160C LEU* 4.6 11.4 - - + -
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Residues in contact with TYR 51 (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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47C ARG 3.1 19.6 + - - +
48C ARG* 4.0 4.7 - - - +
49C ILE 3.3 0.2 - - - -
50C LEU* 1.3 73.8 - - - +
52C GLY* 1.3 60.4 + - - +
54C ASN* 3.1 11.5 + - + +
55C GLU* 2.9 62.3 + - + +
78C TYR* 3.5 39.7 + + - -
136C LEU* 4.5 5.1 - - + +
139C ILE* 4.2 12.8 - - + -
140C ASN* 5.4 1.2 + - - -
146C PHE* 3.5 24.1 - + - -
155C ARG* 3.6 14.9 + - - +
156C GLU* 4.7 0.4 - - + -
157C PRO* 3.5 41.3 - - + -
160C LEU* 5.4 0.7 - - + -
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Residues in contact with GLY 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C ARG 3.1 17.5 + - - -
49C ILE 3.8 2.5 - - - -
50C LEU 3.2 0.2 - - - -
51C TYR* 1.3 77.7 - - - +
53C LEU* 1.3 59.6 + - - +
55C GLU* 3.5 2.9 + - - +
56C GLN* 3.2 31.6 + - - +
58C MET* 4.6 1.3 - - - +
70C ILE* 5.8 2.2 - - - -
73C ASP* 6.3 2.2 - - - -
74C VAL* 4.5 9.6 - - - -
78C TYR* 4.5 14.8 - - - -
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Residues in contact with LEU 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ILE* 3.2 25.2 + - + +
50C LEU* 3.6 26.9 - - + +
51C TYR 3.2 0.2 - - - -
52C GLY* 1.3 76.5 - - - +
54C ASN* 1.3 59.8 + - - +
56C GLN 3.8 0.2 + - - -
57C GLY 3.3 1.7 + - - -
58C MET* 2.8 61.2 + - + +
70C ILE* 3.9 25.8 - - + +
90C MET* 5.5 2.0 - - + -
104C VAL* 4.6 12.1 - - + -
126C ALA* 4.8 1.6 - - + -
127C ARG* 4.2 15.5 - - - +
128C MET* 3.5 27.4 - - + +
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Residues in contact with ASN 54 (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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50C LEU 3.1 13.3 + - - +
51C TYR* 3.1 13.1 + - - +
53C LEU* 1.3 77.0 - - - +
55C GLU* 1.3 81.2 + - - +
57C GLY* 3.3 12.1 + - - -
128C MET* 3.3 12.6 - - - +
133C LEU* 6.0 1.0 - - - +
136C LEU* 3.7 35.9 - - + +
139C ILE* 3.9 20.7 - - - +
140C ASN* 4.2 6.9 - - - +
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Residues in contact with GLU 55 (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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51C TYR* 2.9 57.6 + - + +
52C GLY* 4.2 3.1 - - - +
54C ASN* 1.3 93.8 + - - +
56C GLN* 1.3 72.9 + - - +
57C GLY 3.2 1.2 + - - -
77C LYS* 6.0 0.9 - - - +
78C TYR* 4.3 10.1 - - - +
140C ASN* 4.0 16.6 + - - +
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Residues in contact with GLN 56 (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* 5.8 0.2 - - - +
52C GLY* 3.2 19.3 + - - +
53C LEU 3.8 0.2 + - - -
54C ASN 3.3 0.2 - - - -
55C GLU* 1.3 89.5 + - - +
57C GLY* 1.3 60.7 + - - +
58C MET* 3.3 30.9 + - + +
65C LYS* 5.7 1.9 - - - -
69C ARG* 5.6 3.5 + - - -
73C ASP* 4.2 23.4 + - + +
77C LYS* 3.6 24.7 - - - +
78C TYR* 5.9 0.2 + - - -
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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