Contacts of the helix formed by residues 39 - 50 (chain C) in PDB entry 3PHW
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 ASN 39 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37C ASP* 2.8 19.3 + - - +
38C GLY* 1.3 79.9 + - - +
40C CYS* 1.3 58.2 + - - +
41C PHE 3.3 2.9 - - - -
42C TYR* 2.9 29.2 + - - +
43C HIS* 3.0 24.1 + - + +
58C TYR* 3.3 42.6 + - + -
62C LYS* 4.3 10.3 - - - +
96C ASP* 4.4 1.8 - - - +
97C ASN* 3.3 40.2 + - - +
98C GLU 4.2 3.2 + - - +
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Residues in contact with CYS 40 (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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34C GLN* 4.4 2.2 - - + +
35C PRO 3.7 15.9 - - - +
37C ASP* 3.5 2.0 + - - -
38C GLY 3.5 0.6 - - - -
39C ASN* 1.3 74.4 - - - +
41C PHE* 1.3 68.5 + - - +
43C HIS* 3.7 13.2 - - - +
44C SER* 2.9 28.9 + - - -
151C HIS* 3.8 2.9 - - + -
152C PHE 3.2 34.3 - - - +
75D GLY 3.4 2.7 - - - -
76D NEH 1.8 63.9 - - + -
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Residues in contact with PHE 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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39C ASN 3.1 0.8 + - - -
40C CYS* 1.3 81.9 - - - +
42C TYR* 1.3 86.9 + + + +
44C SER* 3.3 3.6 + - - -
45C ILE* 3.2 46.7 + - + +
100C GLY* 3.8 25.5 - - - +
101C SER 3.7 13.0 - - - -
104C GLU* 3.7 17.7 - - + -
105C ALA* 3.7 31.0 - - + -
108C LEU* 3.9 2.9 - - + -
118C ILE* 4.8 1.3 - - + -
144C LEU* 3.8 24.9 - - + -
152C PHE* 3.5 39.0 - + + -
75D GLY 4.4 0.8 + - - +
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Residues in contact with TYR 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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39C ASN* 2.9 17.2 + - - +
41C PHE* 1.3 93.3 - + + +
43C HIS* 1.3 66.2 + - - +
45C ILE* 3.4 0.7 + - - +
46C ALA* 3.0 24.6 + - - +
58C TYR* 3.8 20.1 - - + +
61C ILE* 3.8 23.8 - - + +
62C LYS* 3.6 37.0 - - + -
65C THR* 3.6 21.1 - - - -
93C MET* 3.7 18.4 + - - +
98C GLU* 3.8 22.3 + - - +
99C TRP 4.5 1.6 + - - -
100C GLY* 3.7 19.5 - - - -
104C GLU* 3.3 22.1 - - + +
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Residues in contact with HIS 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C GLN* 3.5 22.9 - - + +
35C PRO* 3.9 24.7 - - + +
37C ASP* 3.1 27.7 + - - -
39C ASN* 3.0 37.5 + - + +
40C CYS* 3.7 9.4 - - - +
42C TYR* 1.3 75.5 - - - +
44C SER* 1.3 57.4 + - - +
46C ALA* 3.3 5.0 + - - +
47C GLU* 2.9 30.3 + - - +
53C LYS* 3.9 9.1 + - - +
54C THR 4.7 0.2 + - - -
55C ASP* 3.3 23.6 + - + -
58C TYR* 3.3 33.6 - + - +
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Residues in contact with SER 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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34C GLN* 3.4 9.2 - - - +
40C CYS 2.9 21.2 + - - -
41C PHE 3.5 6.5 - - - -
42C TYR 3.2 0.2 - - - -
43C HIS* 1.3 76.7 - - - +
45C ILE* 1.3 64.2 + - - +
47C GLU* 3.4 13.5 - - - +
48C LEU* 3.5 13.7 + - - +
144C LEU* 3.9 16.6 - - - -
152C PHE* 3.3 4.7 + - - -
153C ASP* 3.0 41.9 + - - -
154C ALA* 3.8 5.2 - - - +
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Residues in contact with ILE 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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41C PHE* 3.2 42.1 + - + +
42C TYR 3.4 5.4 + - - +
43C HIS 3.3 0.2 - - - -
44C SER* 1.3 76.8 - - - +
46C ALA* 1.3 62.2 + - - +
48C LEU* 3.1 3.3 + - - +
49C THR* 2.9 43.1 + - + +
61C ILE* 3.8 19.5 - - + -
108C LEU* 3.6 19.3 - - + -
112C MET* 4.2 11.9 - - - -
114C ILE* 5.2 2.0 - - + -
116C ILE* 4.0 18.6 - - + -
142C VAL* 4.8 10.1 - - + -
144C LEU* 4.1 15.3 - - + -
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Residues in contact with ALA 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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42C TYR 3.0 18.1 + - - +
43C HIS* 3.3 5.6 + - - +
45C ILE* 1.3 76.0 - - - +
47C GLU* 1.3 59.1 + - - +
49C THR* 3.9 4.0 - - - -
50C MET* 2.8 56.9 + - - +
53C LYS* 4.0 15.6 - - + +
57C SER* 4.1 7.2 - - - -
58C TYR 4.2 6.3 - - - +
61C ILE* 3.8 10.7 - - + +
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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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32C VAL* 3.6 20.5 - - + +
34C GLN* 3.4 20.9 + - - +
43C HIS 2.9 13.6 + - - +
44C SER 3.4 12.1 - - - +
46C ALA* 1.3 77.2 - - - +
48C LEU* 1.3 58.8 + - + +
49C THR 3.9 0.2 + - - -
50C MET 4.5 5.5 - - - +
53C LYS* 3.5 31.6 + - - +
154C ALA* 3.8 18.8 - - + -
156C ARG* 2.9 37.3 + - - +
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Residues in contact with LEU 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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44C SER 3.8 6.5 - - - +
45C ILE 3.1 7.7 + - - +
47C GLU* 1.3 77.8 - - + +
49C THR* 1.3 62.8 + - - +
50C MET 3.9 0.2 - - - -
142C VAL* 3.6 35.1 - - + +
143C ASN 3.1 32.5 - - - +
144C LEU* 4.1 6.1 - - + -
154C ALA* 3.9 11.0 - - + -
155C LEU 3.5 22.0 - - - +
156C ARG* 3.7 36.9 + - + +
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Residues in contact with THR 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 ILE* 2.9 27.3 + - + +
48C LEU* 1.3 88.1 - - - +
50C MET* 1.3 62.9 + - - +
51C PRO* 3.7 7.5 - - - +
61C ILE* 3.8 10.7 - - - +
112C MET* 3.8 31.6 - - + +
114C ILE* 4.4 5.2 - - + -
142C VAL* 3.6 24.5 - - + -
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Residues in contact with MET 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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46C ALA* 2.8 25.6 + - + +
47C GLU 4.5 4.2 - - - +
48C LEU 3.9 0.4 - - - -
49C THR* 1.3 89.7 - - - +
51C PRO* 1.3 74.3 - - + +
52C ASN 3.7 0.2 + - - -
53C LYS* 3.4 20.0 + - + +
57C SER* 3.6 38.4 - - - +
60C TYR* 3.6 31.6 - - + -
61C ILE* 3.6 22.0 - - + -
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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