Contacts of the strand formed by residues 35 - 50 (chain C) in PDB entry 3W1Y
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 GLN 35 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A ASN* 3.0 29.8 + - - +
33C GLY 5.3 1.6 - - - +
34C ALA* 1.3 75.9 - - - +
36C VAL* 1.3 58.4 + - - +
76C ILE* 3.5 5.4 - - - +
77C VAL* 2.7 53.0 + - + +
78C GLU* 3.5 32.9 + - + +
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Residues in contact with VAL 36 (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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100A ASN* 3.8 17.6 + - - +
101A GLU* 5.2 2.6 - - - +
26C VAL* 4.0 27.4 - - + +
29C ALA* 3.5 33.2 - - + -
30C LYS* 4.0 29.4 + - + +
34C ALA 4.1 0.4 + - - -
35C GLN* 1.3 76.9 - - - +
37C ARG* 1.3 69.9 + - - +
38C GLY 4.0 6.5 + - - +
74C VAL* 3.8 21.5 - - + -
75C ASP 3.4 10.1 - - - +
76C ILE* 4.7 1.3 - - + -
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Residues in contact with ARG 37 (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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38A THR* 3.2 32.3 + - - +
97A PHE* 3.7 42.8 - - + +
100A ASN* 3.6 39.1 + - - +
126A SER* 5.5 4.4 + - - -
5C ARG* 4.0 6.3 - - - +
35C GLN 4.4 0.2 - - - -
36C VAL* 1.3 71.8 - - - +
38C GLY* 1.3 58.7 + - - +
40C ILE* 4.1 3.3 - - - +
74C VAL* 3.8 4.0 - - - -
75C ASP* 2.7 80.3 + - + +
77C VAL* 3.4 28.8 - - + +
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Residues in contact with GLY 38 (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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97A PHE* 4.4 4.5 - - - -
100A ASN 4.3 5.1 + - - -
102A LEU* 5.4 5.2 - - - +
26C VAL* 4.7 3.2 - - - +
30C LYS* 5.2 4.2 + - - -
36C VAL* 4.0 12.5 + - - +
37C ARG* 1.3 74.9 - - - +
39C PRO* 1.3 81.0 - - - +
40C ILE* 3.7 7.9 - - - -
74C VAL* 5.6 0.4 - - - -
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Residues in contact with PRO 39 (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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102A LEU* 3.8 10.4 - - - +
22C THR* 3.4 34.1 - - + -
23C ALA* 5.4 2.0 - - - +
26C VAL* 3.9 19.0 - - + -
38C GLY* 1.3 84.5 - - - +
40C ILE* 1.3 61.5 + - - +
41C PRO* 3.7 8.9 - - + +
72C ARG* 4.9 8.5 - - + -
73C LEU 3.5 7.6 - - - +
74C VAL* 4.5 2.7 - - + -
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Residues in contact with ILE 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PHE* 3.8 43.7 - - + -
97A PHE* 3.5 38.4 - - + -
102A LEU* 4.2 9.0 - - + -
7C ARG* 5.5 0.2 - - - +
37C ARG 4.1 10.3 - - - +
38C GLY* 4.1 2.5 - - - -
39C PRO* 1.3 76.5 - - - +
41C PRO* 1.3 75.2 - - + +
42C LEU* 3.6 8.3 + - + +
72C ARG* 3.3 4.6 - - - -
73C LEU* 2.8 62.0 + - + +
74C VAL 4.8 0.2 - - - +
75C ASP* 4.9 9.2 - - - +
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Residues in contact with PRO 41 (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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102A LEU* 4.5 9.6 - - + -
39C PRO* 3.7 10.1 - - + +
40C ILE* 1.3 91.8 - - + +
42C LEU* 1.3 64.3 + - - +
43C PRO* 4.9 0.2 - - - +
71C LEU 3.8 5.6 - - - +
72C ARG* 3.9 25.3 - - - +
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Residues in contact with LEU 42 (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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93A ALA* 5.2 6.1 - - + -
95A PHE* 4.4 5.4 - - + -
130A GLU* 3.8 31.4 - - + -
132A THR* 5.1 9.9 - - + +
9C ARG* 5.6 4.0 - - + +
40C ILE* 4.3 10.5 - - + +
41C PRO* 1.3 82.2 - - - +
43C PRO* 1.4 78.4 - - + +
44C THR* 3.4 3.3 + - - -
71C LEU* 3.1 45.8 + - + +
72C ARG* 4.1 6.4 + - - -
73C LEU* 3.7 39.3 - - + -
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Residues in contact with PRO 43 (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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93A ALA* 4.9 12.1 - - + -
132A THR* 4.0 24.5 - - + +
72B THR* 5.9 10.5 - - + +
42C LEU* 1.4 89.7 - - + +
44C THR* 1.3 68.5 + - - +
71C LEU* 3.1 21.5 - - - +
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Residues in contact with THR 44 (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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42C LEU 3.4 4.7 + - - -
43C PRO* 1.3 76.8 - - - +
45C ARG* 1.3 64.7 + - - +
46C LYS* 3.6 12.7 + - + +
68C ARG* 3.5 45.1 - - + +
69C THR 3.5 11.4 - - - +
70C HIS* 3.2 33.5 + - + +
71C LEU 5.3 0.2 + - - -
72C ARG* 5.4 1.7 + - - -
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Residues in contact with ARG 45 (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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132A THR* 4.2 25.7 + - + +
43C PRO 3.5 2.2 + - - -
44C THR* 1.3 72.9 - - - +
46C LYS* 1.3 63.4 + - - +
47C GLU* 3.0 35.1 + - - +
67C ILE 3.5 1.3 - - - +
68C ARG* 3.0 10.0 - - - +
69C THR* 2.7 56.0 + - - +
71C LEU* 4.6 12.3 - - + -
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Residues in contact with LYS 46 (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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71B GLU* 3.8 42.5 + - - -
72B THR* 5.0 11.0 - - - -
108B CYS* 4.3 8.7 - - - -
110B GLY* 4.0 16.8 - - - -
111B ASP* 4.3 16.2 + - - +
44C THR* 4.1 10.8 - - + +
45C ARG* 1.3 77.2 - - - +
47C GLU* 1.3 69.1 + - - +
48C ARG* 4.7 10.5 + - - +
66C GLU* 3.2 20.9 - - - +
67C ILE 3.9 0.9 - - - -
68C ARG* 4.5 11.4 - - - +
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Residues in contact with GLU 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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45C ARG* 3.0 42.5 + - - +
46C LYS* 1.3 82.1 - - - +
48C ARG* 1.3 64.0 + - - +
49C PHE* 6.2 2.2 - - + -
66C GLU* 3.3 9.3 - - - +
67C ILE* 2.9 49.1 + - + +
69C THR* 6.0 1.3 - - - +
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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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46C LYS* 4.7 11.1 + - - +
47C GLU* 1.3 77.9 + - - +
49C PHE* 1.3 64.7 + - - +
50C THR* 4.2 2.6 + - - +
64C GLN* 3.2 39.4 + - - +
65C TYR 3.3 10.8 - - - +
66C GLU* 3.0 38.1 + - - +
68C ARG* 5.8 0.2 - - - +
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Residues in contact with PHE 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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47C GLU* 6.0 2.9 - - + -
48C ARG* 1.3 74.4 - - - +
50C THR* 1.3 66.3 + - - +
51C VAL* 3.6 3.1 + - + -
64C GLN* 3.5 3.9 - - - -
65C TYR* 2.7 62.4 + + + +
67C ILE* 3.7 30.5 - - + -
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Residues in contact with THR 50 (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* 4.1 3.3 + - - +
49C PHE* 1.3 74.0 - - - +
51C VAL* 1.3 65.8 + - - +
52C LEU* 3.5 32.7 + - + +
63C ASP 3.7 8.1 - - - +
64C GLN* 2.8 29.6 + - - +
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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