Contacts of the helix formed by residues 40 - 60 (chain A) in PDB entry 5FHX
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 THR 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A THR* 1.3 79.9 - - - +
41A GLU* 1.3 64.2 + - - +
42A LYS* 4.1 6.4 + - - +
43A GLU* 2.9 43.9 + - - +
44A THR* 3.1 13.4 + - - -
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Residues in contact with GLU 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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40A THR* 1.3 73.4 - - - +
42A LYS* 1.3 58.3 + - + +
44A THR* 3.2 7.7 + - - -
45A PHE* 3.1 57.3 + - + -
119A ILE* 5.5 4.7 - - - +
123A LYS* 3.2 46.2 + - - +
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Residues in contact with LYS 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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40A THR* 3.3 7.0 + - - +
41A GLU* 1.3 76.8 - - + +
43A GLU* 1.4 57.4 + - + +
45A PHE* 4.5 1.6 - - + -
46A CYS* 3.2 29.3 + - - +
93A LEU* 3.7 29.3 + - - +
94A ALA* 3.4 19.2 - - - +
95A GLY* 4.7 10.7 - - - +
96A LEU* 5.1 5.1 - - + +
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Residues in contact with GLU 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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39A THR* 3.4 25.0 - - - +
40A THR* 2.9 47.6 + - - +
42A LYS* 1.4 76.4 - - + +
44A THR* 1.3 58.4 + - - +
46A CYS* 3.6 4.9 + - - +
47A ARG* 3.0 39.0 + - - +
96A LEU* 5.9 6.3 - - + -
99A CYS* 4.7 6.5 - - + +
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Residues in contact with THR 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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32A ILE* 3.9 5.8 - - + +
33A PHE* 3.9 30.7 - - + -
39A THR* 3.6 6.9 + - - -
40A THR 3.1 13.2 + - - -
41A GLU* 3.2 11.9 + - - -
43A GLU* 1.3 74.3 - - - +
45A PHE* 1.3 61.3 + - + +
47A ARG* 3.2 25.6 + - - +
48A ALA* 2.8 34.2 + - + +
119A ILE* 5.6 3.8 - - + -
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Residues in contact with PHE 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 GLU* 3.1 57.9 + - + +
42A LYS* 4.0 1.3 - - + +
44A THR* 1.3 80.8 - - + +
46A CYS* 1.3 54.2 + - - +
48A ALA* 3.2 5.4 + - + +
49A ALA* 2.8 37.6 + - - +
90A LEU* 4.2 17.0 - - + +
93A LEU* 3.2 42.2 - - + +
94A ALA* 3.9 18.2 - - + +
116A LEU* 5.7 2.7 - - + -
119A ILE* 5.0 8.5 - - + -
120A MET* 3.8 30.1 - - + -
123A LYS* 4.0 17.3 - - + -
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Residues in contact with CYS 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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42A LYS 3.2 20.0 + - - +
43A GLU* 3.7 7.0 - - - +
45A PHE* 1.3 76.8 - - - +
47A ARG* 1.3 52.3 + - - +
49A ALA 3.6 0.2 + - - -
50A THR* 2.7 36.2 + - - -
91A TRP* 3.7 20.9 - - - -
94A ALA* 3.6 17.2 - - + +
96A LEU* 3.9 15.3 - - + -
97A ASN 4.0 12.8 - - - -
98A SER 4.2 2.2 - - - -
99A CYS* 2.9 36.1 - - + -
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Residues in contact with ARG 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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32A ILE* 3.2 47.1 + - + +
35A ALA 6.4 0.2 - - - -
39A THR* 3.0 29.7 + - - +
43A GLU* 3.0 23.7 + - - +
44A THR* 3.2 23.1 + - - +
46A CYS* 1.3 75.0 - - - +
48A ALA* 1.4 63.3 + - - +
50A THR* 3.6 3.6 + - - -
51A VAL* 3.3 27.5 + - - +
99A CYS* 3.6 24.0 - - + -
100A PRO* 3.9 21.3 - - - +
101A VAL* 4.7 5.1 - - + +
103A GLU* 3.3 21.3 + - - -
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Residues in contact with ALA 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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32A ILE* 3.7 16.1 - - + +
33A PHE* 4.8 1.8 - - + -
44A THR* 2.8 19.9 + - + +
45A PHE* 3.2 8.5 + - + +
47A ARG* 1.4 68.4 - - - +
49A ALA* 1.3 66.8 + - - +
51A VAL* 3.0 15.6 + - - +
52A LEU* 3.1 13.9 + - - +
90A LEU* 4.2 19.5 - - + -
112A PHE* 4.0 16.0 - - + -
116A LEU* 4.7 11.0 - - + -
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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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45A PHE 2.8 19.4 + - - +
46A CYS 3.9 1.6 - - - +
48A ALA* 1.3 71.0 - - - +
50A THR* 1.3 60.1 + - - +
53A ARG* 3.3 9.4 + - - +
87A ASP* 2.5 30.3 - - - +
90A LEU* 3.7 23.8 - - + +
91A TRP* 3.3 40.0 + - + +
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Residues in contact with THR 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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46A CYS 2.7 22.8 + - - -
47A ARG* 3.7 8.5 - - - -
48A ALA 3.1 0.2 - - - -
49A ALA* 1.3 73.8 - - - +
51A VAL* 1.3 60.2 - - + +
53A ARG* 3.2 4.8 - - - +
54A GLN* 3.0 41.2 + - + +
91A TRP* 3.4 18.6 - - - -
97A ASN* 5.1 2.1 + - - -
99A CYS* 3.8 13.7 - - - +
101A VAL* 4.4 22.0 - - + -
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Residues in contact with VAL 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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29A VAL* 3.3 30.0 - - + +
30A THR* 3.7 27.6 - - - +
32A ILE* 3.9 20.9 - - + -
47A ARG 3.3 17.2 + - - +
48A ALA 3.0 5.6 + - - +
50A THR* 1.3 74.6 - - + +
52A LEU* 1.3 58.4 - - - +
54A GLN* 3.5 7.8 - - - +
55A PHE* 3.0 26.2 + - - +
101A VAL* 4.3 12.8 - - + -
112A PHE* 4.3 12.3 - - + -
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Residues in contact with LEU 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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48A ALA 3.1 13.2 + - - +
50A THR 3.3 0.2 - - - -
51A VAL* 1.3 76.1 - - + +
53A ARG* 1.1 69.1 + - - +
55A PHE* 3.0 4.1 + - + +
56A TYR* 2.9 30.3 + - + +
83A LEU* 4.0 22.1 - - + +
86A LEU* 3.6 36.8 - - + -
87A ASP* 3.2 15.7 - - + +
90A LEU* 3.8 17.9 - - + -
109A LEU* 3.8 24.2 - - + -
112A PHE* 3.7 25.6 - - + -
113A LEU* 4.2 4.0 - - + -
116A LEU* 4.9 0.2 - - + -
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Residues in contact with ARG 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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49A ALA 3.3 15.8 + - - +
50A THR* 3.2 6.5 - - - +
52A LEU* 1.1 85.8 - - - +
54A GLN* 0.6 125.8 + - - +
55A PHE* 3.9 0.2 - - - -
56A TYR* 3.9 27.1 + - + +
57A SER* 3.1 19.2 + - - +
87A ASP* 3.3 12.9 + - - +
91A TRP* 3.3 36.0 - - - +
97A ASN* 3.9 25.1 + - - +
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Residues in contact with GLN 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 THR* 3.0 29.8 + - + +
51A VAL* 3.5 9.6 - - - +
53A ARG* 0.6 102.9 + - - +
55A PHE* 1.3 59.4 + - - +
57A SER* 3.7 4.2 + - - -
58A HIS* 2.6 56.7 + - + +
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Residues in contact with PHE 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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24A CYS* 3.7 41.3 - - - -
27A LEU* 4.0 10.3 - - + -
28A THR 3.6 24.9 - - - -
29A VAL* 3.8 15.3 - - + -
51A VAL 3.0 16.9 + - - +
52A LEU* 3.0 7.1 + - + +
53A ARG 2.7 4.6 + - - -
54A GLN* 1.3 72.5 - - - +
56A TYR* 1.4 64.6 + - - +
58A HIS* 3.1 2.2 + - - -
59A HIS* 3.0 61.5 + + + +
80A ILE* 5.5 1.3 - - + -
83A LEU* 3.7 22.4 - - + -
109A LEU* 3.6 30.1 - - + -
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Residues in contact with TYR 56 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A LEU 2.9 24.7 + - - +
53A ARG* 3.9 25.4 + - + -
55A PHE* 1.4 72.6 - - - +
57A SER* 1.3 69.3 + - - +
60A GLU* 3.2 35.3 + - - +
80A ILE* 4.2 20.7 - - + +
83A LEU* 4.0 21.8 - - + -
84A LYS* 3.7 59.6 + - + +
87A ASP* 3.8 26.8 + - + +
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Residues in contact with SER 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 ARG* 3.1 23.3 + - - +
54A GLN* 3.2 6.4 + - - -
56A TYR* 1.3 92.9 - - - +
58A HIS* 1.3 65.2 + - - +
59A HIS 3.5 0.2 - - - -
60A GLU* 4.7 7.5 + - - +
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Residues in contact with HIS 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 GLN* 2.6 57.7 + - + +
55A PHE* 3.1 4.8 + - - +
57A SER* 1.3 83.1 + - - +
59A HIS* 1.4 78.1 + - + +
60A GLU 3.9 0.2 - - - -
61A LYS 5.3 1.3 + - - -
62A ASP* 4.1 7.4 + - - +
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Residues in contact with HIS 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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24A CYS* 4.4 0.7 - - - -
27A LEU* 3.8 13.9 - - + +
28A THR 4.8 3.6 + - - -
55A PHE* 3.0 64.1 + + + +
56A TYR 4.1 0.2 - - - -
58A HIS* 1.4 93.3 + - + +
60A GLU* 1.4 63.3 + - - +
61A LYS 3.1 3.1 - - - -
62A ASP* 2.8 42.4 + - - +
64A ARG* 5.7 1.3 - - - -
65A CYS* 3.6 21.4 - - - +
76A HIS* 3.2 15.7 - - - -
80A ILE* 4.5 2.7 - - + -
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Residues in contact with GLU 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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56A TYR* 3.2 19.6 + - - +
57A SER* 4.7 5.7 + - - +
58A HIS 3.9 0.6 - - - -
59A HIS* 1.4 75.5 - - - +
61A LYS* 1.3 77.8 + - + +
66A LEU* 5.1 2.6 - - - +
76A HIS* 2.9 25.6 + - - +
80A ILE* 3.7 18.9 - - + +
84A LYS* 2.8 31.3 + - - -
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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