Contacts of the helix formed by residues 39 - 58 (chain A) in PDB entry 3PWH
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A ASN 4.3 5.6 + - - -
37A LEU* 2.8 25.3 + - - +
38A GLN* 1.3 74.9 - - - +
40A VAL* 1.3 67.2 + - - +
41A THR* 3.1 31.8 + - - -
42A ASN* 3.3 20.3 + - - +
43A TYR* 3.4 15.9 + - - -
112A TYR* 5.0 2.5 + - - +
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Residues in contact with VAL 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ASN* 1.3 75.8 - - - +
41A THR* 1.3 63.8 + - - +
43A TYR* 3.2 25.8 + - + +
44A PHE* 3.8 9.5 - - + -
112A TYR* 4.7 6.2 + - + +
116A VAL* 3.5 35.4 - - + +
117A THR* 3.3 23.3 - - - +
118A GLY* 3.4 24.2 - - - +
121A ALA* 3.6 13.2 - - + -
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Residues in contact with THR 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ASN* 3.1 15.6 + - - -
40A VAL* 1.3 78.8 - - - +
42A ASN* 1.3 73.1 + - - +
43A TYR 3.1 1.2 + - - -
44A PHE* 3.2 19.7 + - - +
45A VAL* 3.7 9.9 + - + +
98A ILE* 4.9 15.5 - - + +
101A ASP* 2.7 30.7 + - - +
102A ARG* 3.8 20.2 + - - +
112A TYR* 3.1 17.0 + - - -
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Residues in contact with ASN 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A VAL* 4.6 10.4 - - + +
37A LEU* 2.9 37.8 - - - +
39A ASN* 3.3 11.1 + - - +
41A THR* 1.3 87.4 - - - +
43A TYR* 1.3 63.7 + - - +
44A PHE 3.2 0.4 - - - -
45A VAL* 3.4 22.2 - - + +
46A VAL* 3.1 28.0 + - - +
295A PHE* 3.6 32.0 - - - -
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Residues in contact with TYR 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLN* 4.6 15.1 + - + +
39A ASN 3.4 22.7 + - - -
40A VAL* 3.2 25.2 + - + +
41A THR 3.1 0.6 - - - -
42A ASN* 1.3 78.4 - - - +
44A PHE* 1.3 59.5 + - - +
46A VAL* 3.6 10.9 + - + +
47A SER 3.6 9.4 + - - -
118A GLY* 4.1 26.9 - - - -
121A ALA* 4.1 15.5 - - + -
122A ALA* 5.7 3.4 - - + -
125A ILE* 3.1 20.6 - - + +
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Residues in contact with PHE 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A VAL* 3.8 17.0 - - + -
41A THR* 3.2 12.2 + - - +
42A ASN 3.2 0.2 - - - -
43A TYR* 1.3 75.0 - - - +
45A VAL* 1.3 60.1 + - - +
46A VAL 3.1 1.8 - - - -
47A SER* 2.9 21.0 + - - -
48A LEU* 3.0 12.1 + - - +
94A SER* 4.1 13.0 + - - +
97A ALA* 3.6 31.6 - - + -
98A ILE* 4.1 20.0 - - + -
101A ASP* 5.6 8.3 - - + -
116A VAL* 5.6 4.5 - - + -
121A ALA* 3.7 31.6 - - + -
124A ILE* 3.7 28.7 - - + -
125A ILE* 3.6 27.1 - - + -
128A CYS* 5.5 1.6 - - - -
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Residues in contact with VAL 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A VAL* 4.4 12.8 - - + -
31A VAL* 5.9 1.3 - - + -
41A THR* 3.9 7.9 - - + +
42A ASN* 3.2 35.4 + - + +
44A PHE* 1.3 77.7 - - - +
46A VAL* 1.3 58.2 + - + +
48A LEU* 3.2 9.4 + - - +
49A ALA* 2.8 25.3 + - + +
98A ILE* 4.2 18.6 - - + +
238A ILE* 6.2 0.4 - - + -
288A TYR* 3.4 39.9 - - + +
295A PHE* 5.1 8.7 - - + -
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Residues in contact with VAL 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A VAL* 6.3 1.1 - - + -
28A CYS* 4.3 21.8 - - + -
31A VAL* 4.7 24.0 - - + -
42A ASN 3.1 16.8 + - - +
43A TYR* 3.7 13.9 - - + +
45A VAL* 1.3 76.2 - - + +
47A SER* 1.3 57.8 + - - +
49A ALA* 4.1 5.6 - - - -
50A ALA* 2.7 39.2 + - + +
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Residues in contact with SER 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A TYR 3.6 1.6 + - - -
44A PHE* 2.9 20.4 + - - -
46A VAL* 1.3 77.7 - - - +
48A LEU* 1.3 59.2 + - - +
50A ALA* 4.7 3.8 - - - -
51A ALA* 3.2 23.4 + - - +
90A SER* 4.1 1.9 + - - -
94A SER* 3.2 16.2 + - - -
125A ILE* 3.7 25.6 - - - +
128A CYS* 5.7 1.6 - - - +
129A TRP* 3.0 31.1 + - - +
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Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A PHE 3.0 10.6 + - - +
45A VAL* 3.4 8.5 - - - +
47A SER* 1.3 76.2 - - - +
49A ALA* 1.3 59.1 + - - +
51A ALA* 3.4 4.8 - - - +
52A ASP* 3.0 36.1 + - - +
91A SER* 3.4 35.4 - - - +
94A SER* 4.0 10.9 + - - -
95A LEU* 3.6 31.0 - - + -
98A ILE* 5.0 7.0 - - + -
238A ILE* 4.2 4.7 - - + -
242A PHE* 6.0 1.6 - - + -
280A ASN* 6.0 0.9 - - - +
284A ASN* 3.2 25.6 - - - +
288A TYR* 4.1 15.3 - - - +
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Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ASN* 2.9 27.4 + - + +
27A VAL* 4.6 11.7 - - + -
28A CYS* 3.7 22.0 - - - -
45A VAL* 2.8 18.1 + - + +
46A VAL* 3.1 6.7 + - - +
48A LEU* 1.3 74.3 - - - +
50A ALA* 1.3 67.1 - - - +
52A ASP 2.9 3.5 + - - -
53A ILE* 2.8 24.0 + - - +
284A ASN* 6.1 0.2 - - - +
288A TYR* 6.3 0.9 - - + -
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Residues in contact with ALA 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A CYS* 4.5 1.7 - - - -
46A VAL* 2.7 27.5 + - + +
47A SER* 4.3 4.9 - - - +
49A ALA* 1.3 72.9 - - - +
51A ALA* 1.3 60.4 + - - +
53A ILE* 3.3 16.4 - - + +
54A LEU* 3.2 28.5 + - + +
129A TRP* 4.8 7.2 - - + -
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Residues in contact with ALA 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A SER 3.2 21.6 + - - +
48A LEU* 3.4 6.3 - - - +
49A ALA 3.0 0.4 - - - -
50A ALA* 1.3 73.1 - - - +
52A ASP* 1.3 58.9 + - - +
53A ILE 2.9 9.4 + - - -
54A LEU* 3.0 16.3 + - - +
55A VAL* 3.3 13.0 + - - +
87A LEU* 3.7 16.9 - - + +
90A SER* 4.7 2.2 - - - +
91A SER* 4.0 18.2 - - - +
129A TRP* 3.7 23.7 - - + -
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Residues in contact with ASP 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ALA* 3.9 11.8 - - - +
24A ASN* 3.0 22.8 + - - +
48A LEU* 3.0 17.9 + - - +
49A ALA 2.9 2.2 + - - -
51A ALA* 1.3 75.2 - - - +
53A ILE* 1.3 59.6 + - - +
55A VAL* 3.5 22.4 - - - +
87A LEU 5.4 0.7 - - - +
91A SER* 3.7 15.6 + - - -
280A ASN* 3.4 7.7 - - - +
281A SER* 3.3 40.9 + - - +
284A ASN* 3.3 23.9 + - - -
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Residues in contact with ILE 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ALA 4.6 6.3 - - - +
21A ILE* 4.3 14.8 - - + +
24A ASN* 3.3 23.6 - - + -
25A VAL* 4.0 14.8 - - + +
28A CYS* 3.9 18.4 - - - -
49A ALA 2.8 22.8 + - - +
50A ALA* 3.3 20.2 - - + +
51A ALA 2.9 0.2 - - - -
52A ASP* 1.3 75.3 - - - +
54A LEU* 1.3 63.6 + - + +
55A VAL 2.9 8.6 + - - -
56A GLY* 3.2 4.5 + - - -
57A VAL* 3.0 37.3 + - + +
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Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ALA* 3.2 14.6 + - + +
51A ALA 3.0 8.3 + - - +
53A ILE* 1.3 81.9 - - + +
55A VAL* 1.3 54.2 + - - +
57A VAL* 4.1 11.0 - - + -
58A LEU* 2.7 46.1 + - + +
59A ALA 3.0 6.9 + - - -
83A PHE* 4.4 10.5 - - + -
87A LEU* 3.5 29.0 - - + +
129A TRP* 4.5 14.1 - - + -
133A PHE* 6.5 0.4 - - + -
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Residues in contact with VAL 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ALA* 5.5 0.4 - - + -
51A ALA 3.3 15.2 + - - +
52A ASP* 3.5 14.1 - - - +
53A ILE 2.9 1.8 - - - -
54A LEU* 1.3 76.5 - - - +
56A GLY* 1.3 58.5 + - - +
59A ALA* 2.9 22.8 + - + -
60A ILE* 2.7 46.5 + - + -
84A VAL* 6.1 2.7 - - + -
87A LEU* 3.6 16.6 - - + -
246A TRP* 6.6 0.2 - - + -
278A HIS* 4.3 15.0 - - + +
281A SER* 3.3 27.8 - - - +
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Residues in contact with GLY 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ALA* 3.5 44.9 - - - +
20A ALA* 4.5 3.3 - - - +
21A ILE* 4.1 8.6 - - - +
52A ASP 4.0 3.4 + - - -
53A ILE 3.2 6.0 + - - -
55A VAL* 1.3 79.8 - - - +
57A VAL* 1.3 62.2 + - - +
60A ILE* 3.9 5.6 - - - -
61A PRO* 3.5 10.3 - - - +
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Residues in contact with VAL 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ILE* 3.6 26.7 - - + -
53A ILE* 3.0 30.0 + - + +
54A LEU* 4.1 12.3 - - + -
55A VAL 3.1 0.6 - - - -
56A GLY* 1.3 80.0 - - - +
58A LEU* 1.3 76.3 + - + +
61A PRO* 3.1 14.9 - - - +
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Residues in contact with LEU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU* 2.7 31.4 + - + +
55A VAL 3.4 0.2 + - - -
57A VAL* 1.3 95.3 - - + +
59A ALA* 1.3 55.0 + - - +
61A PRO* 3.1 6.4 - - + +
62A PHE* 2.8 63.3 + - + -
79A PHE* 5.8 1.8 - - + -
83A PHE* 3.5 33.9 - - + -
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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