Contacts of the helix formed by residues 58 - 77 (chain A) in PDB entry 4F4I
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 58 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A ASP 3.7 2.6 + - - -
57A MET* 1.3 79.4 - - - +
59A ILE* 1.3 62.3 + - - +
60A ARG* 2.9 38.5 + - - +
61A THR* 3.6 16.6 + - - +
62A GLU* 3.1 24.9 + - - +
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Residues in contact with ILE 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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57A MET 4.2 4.0 - - - +
58A ASP* 1.3 76.4 + - - +
60A ARG* 1.3 65.4 + - + +
62A GLU* 3.4 8.8 - - - +
63A ALA* 3.0 26.3 + - - +
101A GLN* 5.2 2.5 - - + +
105A ARG* 3.7 52.0 - - + +
106A GLY 5.4 0.7 - - - -
107A ILE* 3.6 34.2 - - + +
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Residues in contact with ARG 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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58A ASP* 2.9 11.6 + - - +
59A ILE* 1.3 79.7 - - + +
61A THR* 1.3 56.1 + - - +
62A GLU 3.2 1.3 - - - -
63A ALA* 3.1 8.7 + - - +
64A MET* 2.7 47.5 + - + +
107A ILE* 4.2 36.8 + - + +
111A GLU* 3.6 36.8 + - - +
115A LEU* 5.2 0.2 - - - +
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Residues in contact with THR 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 MET* 4.0 21.3 - - + -
58A ASP* 3.6 25.3 + - - +
60A ARG* 1.3 74.9 - - - +
62A GLU* 1.3 64.3 + - - +
64A MET* 3.1 21.5 + - + +
65A LEU* 2.9 41.2 + - + +
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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
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51A VAL* 3.3 36.3 - - + +
54A GLY* 5.6 0.5 - - - -
57A MET* 3.5 38.7 + - + +
58A ASP 3.1 13.6 + - - +
59A ILE* 3.4 11.3 - - - +
61A THR* 1.3 79.9 - - - +
63A ALA* 1.3 57.4 + - - +
65A LEU* 3.4 3.6 + - - +
66A PHE* 2.9 40.9 + - + -
101A GLN* 5.4 1.0 + - - +
105A ARG* 2.8 30.9 + - - -
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Residues in contact with ALA 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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59A ILE 3.0 15.4 + - - +
60A ARG* 3.1 9.1 + - - +
62A GLU* 1.3 73.5 - - - +
64A MET* 1.3 62.7 + - - +
66A PHE* 3.2 11.3 + - - +
67A ALA* 3.1 16.6 + - - +
101A GLN* 4.0 20.0 - - + +
107A ILE* 4.2 15.7 - - + -
112A VAL* 5.6 4.3 - - + -
115A LEU* 3.7 21.5 - - + +
116A ASN* 5.9 0.5 + - - -
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Residues in contact with MET 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 ARG* 2.7 21.8 + - + +
61A THR* 3.1 35.2 + - + +
63A ALA* 1.3 68.9 - - - +
65A LEU* 1.3 60.6 + - + +
67A ALA* 2.8 24.1 + - - +
68A ALA* 3.0 13.0 + - - +
115A LEU* 4.2 26.2 - - + -
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Residues in contact with LEU 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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47A ILE* 3.2 29.8 - - + +
50A ILE* 4.4 20.2 - - + -
51A VAL* 3.6 28.5 - - + -
57A MET* 4.0 10.1 - - + -
61A THR* 2.9 36.4 + - + +
62A GLU 3.6 6.5 - - - +
64A MET* 1.3 76.7 - - + +
66A PHE* 1.3 64.5 + - - +
68A ALA* 3.3 5.3 + - + -
69A SER* 3.1 21.1 + - - -
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Residues in contact with PHE 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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37A GLU* 5.1 1.0 - - - +
48A ARG* 3.8 49.6 + - + -
51A VAL* 4.3 26.5 - - + -
62A GLU* 2.9 30.4 + - + -
63A ALA* 3.4 8.7 - - - +
64A MET 3.1 0.8 - - - -
65A LEU* 1.3 78.5 - - - +
67A ALA* 1.3 56.1 + - - +
69A SER* 4.1 3.7 - - - -
70A ARG* 3.2 37.0 + - - +
97A SER* 5.6 0.4 - - - +
101A GLN* 3.1 40.2 - - - +
105A ARG* 6.0 0.4 - - - -
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Residues in contact with ALA 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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63A ALA 3.1 10.0 + - - +
64A MET 2.8 13.4 + - - +
66A PHE* 1.3 71.8 - - - +
68A ALA* 1.3 56.9 + - - +
70A ARG* 3.1 12.3 - - - +
71A ARG* 2.8 31.4 + - - +
115A LEU* 4.2 23.6 - - + -
116A ASN* 4.3 7.2 - - - +
119A ALA* 3.6 27.8 - - + +
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Residues in contact with ALA 68 (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 ILE* 4.0 16.6 - - + -
64A MET 3.0 10.3 + - - +
65A LEU* 3.7 12.8 - - + +
67A ALA* 1.3 77.4 - - - +
69A SER* 1.3 56.4 + - - +
71A ARG* 3.1 5.6 + - - +
72A GLU* 2.9 33.5 + - + +
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Residues in contact with SER 69 (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 GLU* 5.4 1.9 - - - +
38A PRO* 3.7 14.2 - - - +
44A GLY* 3.2 24.0 + - - -
47A ILE* 3.7 23.9 - - - +
48A ARG* 4.5 17.9 + - - -
65A LEU 3.1 16.9 + - - -
66A PHE* 4.1 4.7 - - - -
68A ALA* 1.3 73.3 - - - +
70A ARG* 1.3 64.1 - - - +
72A GLU* 3.7 2.3 + - - +
73A HIS* 3.0 23.2 + - - +
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Residues in contact with ARG 70 (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 GLU* 2.7 49.6 + - - +
66A PHE* 3.2 35.6 + - - +
67A ALA* 3.1 12.7 + - - +
69A SER* 1.3 80.2 - - - +
71A ARG* 1.3 57.1 + - - +
73A HIS* 2.9 6.3 + - - +
74A LEU* 2.8 28.9 + - + +
92A ARG* 4.6 0.8 - - - +
93A TYR* 2.9 43.9 + - + +
94A ILE 4.2 1.1 - - - +
96A SER* 4.8 3.6 - - - -
97A SER* 2.8 24.0 + - - -
116A ASN* 3.4 19.1 + - - -
119A ALA* 4.5 3.6 - - + -
120A ILE* 4.2 24.5 - - + -
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Residues in contact with ARG 71 (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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67A ALA 2.8 17.9 + - - +
68A ALA* 3.1 5.3 + - - +
70A ARG* 1.3 70.8 - - - +
72A GLU* 1.3 65.9 + - - +
74A LEU* 3.9 15.5 - - - +
75A VAL* 2.9 52.7 + - + +
79A ILE* 5.3 3.4 - - - +
118A PHE* 4.8 7.6 - - - -
119A ALA* 2.6 52.1 + - - +
120A ILE 3.8 14.5 + - - -
121A ASN* 3.8 25.3 - - - +
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Residues in contact with GLU 72 (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 VAL* 4.8 2.9 - - + -
43A THR* 2.6 46.4 + - - +
44A GLY* 4.0 9.2 - - - +
47A ILE* 4.1 11.7 - - + -
68A ALA* 2.9 19.5 + - + +
69A SER 3.8 4.7 - - - +
71A ARG* 1.3 79.3 - - - +
73A HIS* 1.3 56.7 + - - +
75A VAL* 5.4 4.0 - - - +
76A LEU* 2.8 51.9 + - + +
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Residues in contact with HIS 73 (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* 2.7 45.7 + - + +
37A GLU* 3.5 32.7 - - + +
38A PRO* 3.2 32.1 - - + +
39A GLY* 3.8 4.0 - - - -
41A VAL* 4.4 8.5 - - + +
69A SER 3.0 15.0 + - - +
70A ARG 2.9 10.0 + - - +
72A GLU* 1.3 74.4 - - - +
74A LEU* 1.3 58.0 + - - +
77A LYS* 3.0 44.6 + - + +
78A VAL* 3.1 21.7 + - + +
90A CYS* 4.5 5.0 - - - -
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Residues in contact with LEU 74 (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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4A PHE* 5.1 0.2 - - + -
70A ARG* 2.8 19.0 + - + +
71A ARG* 3.9 17.7 - - - +
73A HIS* 1.3 74.9 + - - +
75A VAL* 1.3 57.4 + - - +
78A VAL* 3.3 21.1 + - + +
79A ILE* 2.6 47.5 + - + +
93A TYR* 3.8 19.3 - - + +
119A ALA 3.9 2.5 - - - +
120A ILE* 3.5 39.9 - - + +
123A LEU* 2.7 35.2 - - + -
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Residues in contact with VAL 75 (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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71A ARG* 2.9 53.0 + - + +
72A GLU* 5.4 4.7 - - - +
74A LEU* 1.3 77.6 - - + +
76A LEU* 1.3 75.8 + - + +
77A LYS 3.5 0.2 - - - -
79A ILE* 3.7 23.3 - - + +
80A PRO* 3.2 18.6 - - - +
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Residues in contact with LEU 76 (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 VAL* 3.9 21.2 - - + +
43A THR* 3.8 11.4 - - + +
72A GLU* 2.8 41.3 + - - +
75A VAL* 1.3 92.9 - - + +
77A LYS* 1.3 61.1 + - - +
80A PRO* 3.7 11.7 - - - +
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Residues in contact with LYS 77 (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 ILE* 4.5 18.8 - - + +
34A MET 4.4 4.9 + - - -
35A THR* 2.7 34.1 + - + +
39A GLY* 2.8 31.2 + - - +
41A VAL* 4.0 13.2 - - + -
73A HIS* 3.0 24.9 + - + +
75A VAL 3.5 0.6 - - - -
76A LEU* 1.3 80.7 - - - +
78A VAL* 1.3 67.2 + - + +
79A ILE 3.5 0.9 - - - -
80A PRO* 3.6 4.3 - - - +
81A ALA* 3.3 23.4 + - - +
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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