Contacts of the helix formed by residues 34 - 50 (chain A) in PDB entry 1PHP
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 ASP 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A VAL* 4.5 4.3 - - - -
31A ILE* 3.9 15.0 - - + +
33A ASP* 1.3 73.9 + - - +
35A THR* 1.3 62.3 + - - +
36A ARG 3.2 3.4 - - - -
37A ILE* 3.1 25.8 + - + -
38A ARG* 2.9 43.4 + - - +
79A ARG* 2.6 46.9 + - + +
83A LEU* 4.4 0.9 - - - +
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Residues in contact with THR 35 (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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33A ASP* 2.5 28.7 + - - -
34A ASP* 1.3 73.5 - - - +
36A ARG* 1.3 64.1 + - + +
38A ARG* 3.3 26.8 + - - +
39A ALA* 3.0 28.9 + - + +
358A GLU* 5.9 3.6 - - - +
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Residues in contact with ARG 36 (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 ASP* 3.4 47.1 + - + +
23A ASN* 2.5 58.6 + - - +
24A VAL* 4.3 13.6 - - + +
25A PRO* 5.7 2.2 - - - -
33A ASP 5.0 0.4 + - - -
34A ASP 3.1 1.4 + - - -
35A THR* 1.3 78.5 - - + +
37A ILE* 1.3 65.9 + - - +
39A ALA* 3.4 9.9 + - + +
40A ALA* 3.4 18.2 + - - +
170A LEU* 5.6 0.5 - - - +
371A THR 4.8 11.1 + - - -
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Residues in contact with ILE 37 (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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22A PHE* 3.8 26.4 - - + -
24A VAL* 4.0 20.4 - - + -
31A ILE* 4.0 26.9 - - + -
34A ASP* 3.1 11.5 + - + +
36A ARG* 1.3 74.7 - - - +
38A ARG* 1.4 64.8 + - - +
40A ALA* 3.1 17.0 + - - +
41A LEU* 3.6 8.8 + - - +
76A VAL* 4.1 16.6 - - + -
79A ARG* 4.1 13.5 - - + -
80A LEU* 3.8 30.1 - - + -
83A LEU* 3.7 22.7 - - + -
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Residues in contact with ARG 38 (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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33A ASP* 4.4 2.0 + - - -
34A ASP* 2.9 31.2 + - - +
35A THR* 3.3 34.6 + - - +
37A ILE* 1.4 77.5 - - - +
39A ALA* 1.3 60.1 + - - +
41A LEU* 3.2 29.2 + - + +
42A PRO* 4.0 3.6 - - - +
79A ARG* 5.0 2.7 - - - +
83A LEU* 3.9 33.0 - - + -
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Residues in contact with ALA 39 (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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35A THR* 3.0 19.1 + - + +
36A ARG* 3.6 10.8 - - + +
37A ILE 3.3 0.2 - - - -
38A ARG* 1.3 75.2 - - - +
40A ALA* 1.3 59.0 + - - +
42A PRO* 3.6 12.2 - - - +
144A ASP* 5.3 0.3 - - - +
170A LEU* 3.6 38.0 - - + +
371A THR* 5.4 7.6 - - + -
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Residues in contact with ALA 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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20A VAL* 4.5 13.2 - - + -
21A ASP 5.6 1.1 - - - +
22A PHE* 3.5 25.6 - - + -
36A ARG 3.4 5.0 + - - +
37A ILE 3.1 11.0 + - - +
39A ALA* 1.3 77.6 - - - +
41A LEU* 1.3 62.7 + - - +
42A PRO* 3.5 1.1 - - - -
43A THR* 3.3 8.0 + - - -
44A ILE* 3.2 31.4 + - + +
144A ASP* 4.9 6.3 - - - +
170A LEU* 4.5 6.5 - - + +
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Residues in contact with LEU 41 (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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37A ILE 3.6 8.5 - - - +
38A ARG* 3.2 26.8 + - + +
40A ALA* 1.3 75.6 - - - +
42A PRO* 1.3 61.2 - - + +
44A ILE* 3.0 4.5 + - + -
45A ARG* 2.7 69.6 + - - +
80A LEU* 3.8 21.5 - - + -
83A LEU* 4.2 24.0 - - + +
84A LEU* 3.5 29.4 - - + -
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Residues in contact with PRO 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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38A ARG 4.0 4.0 - - - +
39A ALA 3.6 12.8 - - - +
40A ALA 3.5 4.0 - - - -
41A LEU* 1.3 93.1 - - + +
43A THR* 1.3 61.5 + - - +
45A ARG* 4.0 10.4 - - + +
46A TYR* 3.1 24.8 + - - +
169A PHE* 3.8 23.3 - - + -
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Residues in contact with THR 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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6A ILE* 4.1 14.3 - - + +
18A CYS* 4.1 26.0 - - - -
20A VAL* 5.8 0.4 - - + -
40A ALA 3.3 6.8 + - - -
41A LEU 3.2 0.4 - - - -
42A PRO* 1.3 78.4 - - - +
44A ILE* 1.3 66.1 + - + +
46A TYR* 3.3 3.8 + - - +
47A LEU* 3.1 29.6 + - + +
142A VAL* 4.5 1.8 - - + -
144A ASP* 2.6 31.8 + - + +
168A GLY* 4.2 5.8 - - - -
169A PHE* 3.0 29.6 + - - +
170A LEU 4.2 0.2 + - - -
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Residues in contact with ILE 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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18A CYS* 5.4 0.9 - - - -
20A VAL* 4.8 4.7 - - + -
22A PHE* 4.0 19.1 - - + -
40A ALA* 3.2 32.3 + - + +
41A LEU* 3.0 9.2 + - - +
43A THR* 1.3 77.5 - - + +
45A ARG* 1.3 66.1 + - - +
47A LEU* 3.2 9.7 + - + +
48A ILE* 3.0 40.7 + - + +
54A VAL* 4.9 8.7 - - + +
56A LEU* 4.1 27.8 - - + -
80A LEU* 4.2 11.2 - - + -
84A LEU* 4.2 18.2 - - + -
111A VAL* 4.7 6.7 - - + -
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Residues in contact with ARG 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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41A LEU* 2.7 52.7 + - - +
42A PRO* 4.0 9.0 - - + +
44A ILE* 1.3 74.0 - - - +
46A TYR* 1.3 64.2 + - - +
48A ILE* 3.3 10.1 + - + +
49A GLU* 2.9 41.3 + - + +
83A LEU 3.9 19.4 + - - -
84A LEU* 4.2 17.9 - - - +
85A GLU* 5.5 1.4 + - - -
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Residues in contact with TYR 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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6A ILE* 3.6 36.2 + - + -
7A ARG* 3.6 30.9 + - + +
9A VAL 5.4 1.1 + - - -
11A VAL* 5.0 5.6 - - + -
42A PRO 3.1 16.6 + - - +
43A THR 3.5 4.5 - - - +
44A ILE 3.2 0.2 - - - -
45A ARG* 1.3 79.6 - - - +
47A LEU* 1.3 67.9 + - + +
49A GLU* 3.4 5.7 + - - +
50A HIS* 2.8 72.7 + + + +
169A PHE* 3.7 26.9 - + + -
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Residues in contact with LEU 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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6A ILE* 4.3 22.4 - - + -
11A VAL* 4.1 31.0 - - + -
16A VAL* 4.2 22.4 - - + -
18A CYS* 4.3 12.8 - - - -
43A THR* 3.1 29.4 + - + +
44A ILE* 3.7 7.2 - - - +
46A TYR* 1.3 76.6 - - + +
48A ILE* 1.3 64.9 + - - +
50A HIS* 3.4 2.4 + - - +
51A GLY 3.3 4.3 + - - -
52A ALA* 3.0 32.9 + - + +
54A VAL* 3.8 26.0 - - + -
142A VAL* 4.8 2.5 - - + -
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Residues in contact with ILE 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 ILE* 3.0 29.5 + - + +
45A ARG* 3.6 10.5 - - + +
47A LEU* 1.3 74.6 - - - +
49A GLU* 1.3 67.6 - - + +
51A GLY* 3.1 12.0 + - - -
54A VAL* 4.4 7.4 - - + -
84A LEU* 4.2 10.3 - - + -
86A ARG* 3.5 37.0 - - - +
109A GLY* 3.5 37.3 - - - +
111A VAL* 3.7 27.6 - - + -
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Residues in contact with GLU 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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12A ARG* 4.4 8.3 + - - -
45A ARG* 2.9 32.2 + - + +
46A TYR* 3.6 7.5 - - - +
48A ILE* 1.3 81.3 - - + +
50A HIS* 1.3 75.0 + - + +
51A GLY 3.5 1.0 + - - -
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Residues in contact with HIS 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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11A VAL* 3.6 19.5 - - + +
12A ARG* 3.3 48.2 + - - +
46A TYR* 2.8 68.2 + + - +
48A ILE 3.2 0.4 - - - -
49A GLU* 1.3 95.7 - - + +
51A GLY* 1.3 56.0 + - - +
52A ALA 3.5 1.6 - - - -
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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