Contacts of the helix formed by residues 52 - 67 (chain A) in PDB entry 4M3P
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 HIS 52 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A TYR* 3.7 33.7 - + + -
48A ALA* 2.8 16.4 + - - +
51A GLU* 1.3 107.8 + - + +
53A PRO* 1.3 68.3 - - - +
54A GLU* 3.1 27.1 - - - +
55A ALA* 3.1 12.2 + - + +
56A VAL* 3.5 8.1 + - - +
65B ARG* 3.5 33.7 + - - -
326B GLU* 4.4 6.3 - - - -
327B LYS* 5.8 0.8 - - - -
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Residues in contact with PRO 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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48A ALA 3.3 6.0 - - - +
49A ALA 3.6 13.9 - - - +
50A VAL 3.3 18.4 - - - +
51A GLU 3.6 2.0 - - - +
52A HIS* 1.3 89.4 - - - +
54A GLU* 1.3 63.7 + - + +
56A VAL* 3.2 3.2 + - + +
57A ARG* 2.8 48.4 + - - +
106A ILE* 3.9 15.6 - - + +
501B SRT 6.1 0.2 - - - +
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Residues in contact with GLU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A TYR* 4.9 3.6 + - - -
51A GLU 4.8 0.3 - - - +
52A HIS* 3.2 36.0 - - - +
53A PRO* 1.3 94.6 - - - +
55A ALA* 1.3 55.4 + - - +
57A ARG* 3.7 12.0 - - - +
58A GLN* 3.1 31.4 + - - +
58B GLN* 3.7 18.9 - - - +
61B ARG* 4.5 13.9 - - - +
501B SRT 3.5 34.7 + - - +
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Residues in contact with ALA 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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33A LEU* 4.0 10.4 - - + +
36A ARG* 5.6 0.9 + - - -
38A TYR* 3.5 47.1 - - + -
52A HIS* 3.1 11.5 + - + +
54A GLU* 1.3 79.8 - - + +
56A VAL* 1.3 65.5 + - + +
58A GLN* 3.6 2.1 + - - +
59A LEU* 3.2 21.7 + - - +
58B GLN* 3.6 15.4 - - - +
62B GLU* 5.0 1.2 - - - +
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Residues in contact with VAL 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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29A PHE* 4.1 5.1 - - + -
33A LEU* 4.1 11.0 - - + -
48A ALA* 3.8 43.1 - - + +
49A ALA* 3.9 5.4 - - + +
52A HIS 3.9 0.7 - - - +
53A PRO 3.2 6.4 + - - +
55A ALA* 1.3 74.4 - - + +
57A ARG* 1.3 67.0 + - - +
59A LEU* 3.2 4.4 + - - +
60A HIS* 3.0 44.2 + - + +
74A PHE* 4.0 26.9 - - + -
103A ALA* 5.8 1.1 - - - -
106A ILE* 4.4 14.8 - - + -
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Residues in contact with ARG 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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53A PRO* 2.8 35.2 + - - +
54A GLU* 3.7 17.4 - - - +
56A VAL* 1.3 78.1 - - - +
58A GLN* 1.3 55.8 + - - +
60A HIS* 3.3 4.5 + - - +
61A ARG* 2.9 63.6 + - - +
106A ILE* 3.5 26.9 - - + +
109A GLN* 2.8 28.8 + - - +
110A VAL* 3.8 17.2 - - + +
501B SRT 3.4 24.0 + - - -
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Residues in contact with GLN 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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36A ARG* 5.3 2.0 - - - +
54A GLU 3.1 18.9 + - - +
55A ALA 4.0 4.0 - - - +
56A VAL 3.3 0.2 - - - -
57A ARG* 1.3 77.0 - - - +
59A LEU* 1.3 57.4 + - - +
61A ARG* 3.2 15.5 + - - +
62A GLU* 2.9 58.9 + - - +
36B ARG* 6.0 0.2 - - - +
38B TYR* 3.0 31.6 + - - -
54B GLU* 3.6 23.3 - - - +
55B ALA* 3.6 17.1 - - - +
58B GLN* 4.0 29.4 - - + -
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Residues in contact with LEU 59 (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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29A PHE* 3.5 33.9 - - + -
32A ALA* 4.0 16.4 - - + -
33A LEU* 3.9 21.8 - - + -
36A ARG* 3.6 34.7 - - - +
55A ALA 3.2 17.5 + - - +
56A VAL 3.2 3.6 + - - +
58A GLN* 1.3 72.5 - - - +
60A HIS* 1.3 67.1 + - - +
62A GLU* 3.1 11.3 + - - +
63A PHE* 3.0 49.4 + - + -
304A PRO* 4.4 3.6 - - + -
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Residues in contact with HIS 60 (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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26A ASP* 4.6 0.4 + - - -
29A PHE* 3.3 27.1 - + - -
56A VAL* 3.0 37.3 + - + +
57A ARG 3.4 8.1 - - - +
59A LEU* 1.3 76.5 - - - +
61A ARG* 1.3 59.9 + - - +
63A PHE* 3.2 3.1 + - - +
64A LEU* 2.9 24.4 + - - +
71A MET* 3.6 28.4 - - + +
72A GLN 3.1 29.5 + - - -
74A PHE* 4.6 6.8 + - - +
103A ALA 4.8 1.8 + - - -
106A ILE* 3.9 15.3 - - + -
107A ALA* 4.1 22.6 + - + +
110A VAL* 3.7 19.1 - - + -
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Residues in contact with ARG 61 (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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57A ARG* 2.9 42.3 + - - +
58A GLN* 3.5 24.7 + - - +
59A LEU 3.2 0.2 - - - -
60A HIS* 1.3 78.0 - - - +
62A GLU* 1.3 56.7 + - - +
64A LEU* 3.6 4.8 - - + +
65A ARG* 3.0 29.6 + - - +
109A GLN* 3.6 19.6 - - - +
110A VAL* 3.8 11.6 - - + +
113A GLU* 2.6 43.5 + - - +
38B TYR* 4.4 5.5 + - - +
54B GLU* 4.8 19.0 - - - +
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Residues in contact with GLU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ARG* 2.8 42.1 + - - -
58A GLN* 2.9 48.8 + - - +
59A LEU* 3.1 7.0 + - - +
61A ARG* 1.3 73.5 - - - +
63A PHE* 1.3 60.7 + - - +
65A ARG* 3.4 4.8 + - - +
66A ALA* 3.0 28.8 + - - +
304A PRO* 3.5 23.6 - - + +
36B ARG* 3.5 33.7 + - - +
38B TYR* 3.4 10.9 - - + +
55B ALA* 5.1 0.7 - - - +
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Residues in contact with PHE 63 (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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26A ASP* 3.8 6.7 - - + -
27A GLY* 3.4 33.0 - - - -
28A GLY 3.9 2.2 - - - -
29A PHE* 3.5 35.9 - + - -
32A ALA* 5.3 1.1 - - + -
59A LEU* 3.0 42.6 + - + -
60A HIS* 3.7 5.4 - - - +
62A GLU* 1.3 77.9 - - - +
64A LEU* 1.3 60.4 + - - +
66A ALA* 3.1 10.5 + - - +
67A GLY 3.1 1.0 + - - -
68A SER* 3.0 34.6 + - - +
71A MET* 4.6 2.0 - - + -
302A PHE 3.6 11.0 - - - -
303A GLU* 3.7 7.6 - - - -
304A PRO* 3.6 27.6 - - + -
307A ILE* 3.6 19.1 - - + -
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Residues in contact with LEU 64 (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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60A HIS 2.9 13.6 + - - +
61A ARG* 3.6 9.9 - - + +
63A PHE* 1.3 74.8 - - - +
65A ARG* 1.3 56.6 + - - +
67A GLY* 3.0 20.8 + - - -
68A SER 3.7 10.8 + - - +
71A MET* 3.7 12.4 - - + +
110A VAL* 3.3 31.0 - - + +
113A GLU* 3.8 28.9 - - + +
114A GLY* 4.2 13.0 - - - -
115A ASP 4.5 1.8 - - - +
116A ALA* 3.6 31.4 - - + -
323A PRO* 4.5 4.9 - - - +
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Residues in contact with ARG 65 (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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61A ARG 3.0 16.9 + - - +
62A GLU 3.7 4.9 - - - +
63A PHE 3.3 0.2 - - - -
64A LEU* 1.3 77.1 - - - +
66A ALA* 1.3 56.0 + - - +
323A PRO* 3.2 39.6 + - + +
324A ALA* 2.8 36.9 + - + +
326A GLU* 2.9 30.1 + - - +
327A LYS* 3.5 13.7 - - - +
36B ARG 4.9 1.8 - - - +
37B GLY 2.8 31.0 + - - -
38B TYR* 3.4 33.2 - - - -
52B HIS* 3.4 29.0 + - - -
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Residues in contact with ALA 66 (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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62A GLU 3.0 17.7 + - - +
63A PHE* 3.1 7.8 + - - +
65A ARG* 1.3 76.6 - - - +
67A GLY* 1.3 56.6 + - - +
304A PRO* 3.2 29.8 - - + +
307A ILE* 3.8 10.0 - - + +
308A ARG* 3.3 26.0 + - + +
311A ALA* 3.7 4.5 - - - +
322A PRO* 3.2 12.6 - - - +
324A ALA* 4.0 12.5 - - + +
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Residues in contact with GLY 67 (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 ILE* 3.6 21.8 - - - +
64A LEU 3.0 9.9 + - - -
65A ARG 3.2 1.0 - - - -
66A ALA* 1.3 81.1 - - - +
68A SER* 1.3 68.3 + - - +
69A ASN* 3.4 10.9 + - - +
311A ALA* 4.5 4.7 - - - -
318A ARG* 4.6 4.1 + - - -
320A PHE* 6.5 0.7 - - - -
322A PRO* 3.5 15.9 - - - -
323A PRO* 5.1 1.1 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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