Contacts of the helix formed by residues 75 - 90 (chain A) in PDB entry 3REO
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 GLU 75 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ASN* 3.1 18.3 + - - +
74A PRO* 1.3 84.5 - - - +
76A ALA* 1.3 65.5 + - - +
77A PRO 3.3 1.6 - - - -
78A VAL* 3.1 23.5 + - + +
79A MET* 3.0 37.2 + - + +
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Residues in contact with ALA 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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66A ALA* 4.3 9.9 - - + -
69A LEU* 5.2 1.3 - - + -
71A THR* 4.1 18.8 - - + -
73A ASN* 3.0 22.1 + - - +
75A GLU* 1.3 76.8 - - - +
77A PRO* 1.4 59.4 - - + +
79A MET* 3.2 4.1 + - - +
80A LEU* 2.8 32.3 + - - +
150C ILE* 3.7 30.6 - - + +
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Residues in contact with PRO 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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62A PRO* 3.5 10.5 - - + +
63A ALA* 4.0 27.8 - - + +
66A ALA* 3.9 20.8 - - + -
73A ASN 4.1 2.0 - - - +
74A PRO* 3.5 14.6 - - + +
75A GLU 3.5 3.8 - - - -
76A ALA* 1.4 94.0 - - + +
78A VAL* 1.3 59.2 + - + +
80A LEU* 3.3 1.5 + - + +
81A ASP* 2.8 30.7 + - - +
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Residues in contact with VAL 78 (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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74A PRO 5.3 0.9 + - - +
75A GLU* 3.1 25.6 + - + +
77A PRO* 1.3 82.6 - - + +
79A MET* 1.3 67.0 + - + +
81A ASP* 3.2 10.2 + - + +
82A ARG* 3.1 43.3 + - + +
331C LYS* 6.4 1.8 - - + -
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Residues in contact with MET 79 (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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73A ASN* 3.8 23.6 - - - -
75A GLU* 3.0 31.4 + - + +
76A ALA 3.8 4.7 - - - +
78A VAL* 1.3 79.6 - - + +
80A LEU* 1.3 63.6 + - - +
82A ARG* 3.4 5.6 + - - +
83A VAL* 3.1 28.0 + - - +
146C LEU* 4.7 4.0 - - + -
149C ALA* 3.7 17.0 - - + +
150C ILE* 3.6 43.3 - - + +
153C GLY* 5.8 0.2 - - - -
154C GLY 4.4 8.5 - - - +
156C PRO* 5.3 2.0 - - + -
324C LEU* 3.7 33.9 - - + +
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Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ALA* 6.1 1.1 - - + -
44A LEU* 4.3 16.8 - - + -
46A VAL* 3.7 25.4 - - + -
62A PRO* 4.0 9.2 - - + +
65A ILE* 3.8 22.9 - - + -
66A ALA* 3.9 19.7 - - + +
69A LEU* 3.6 26.0 - - + -
76A ALA 2.8 16.2 + - - +
77A PRO 3.5 4.9 - - - +
79A MET* 1.3 73.8 - - - +
81A ASP* 1.3 59.1 + - - +
83A VAL* 3.2 9.4 + - + +
84A LEU* 2.8 41.0 + - + +
150C ILE* 4.5 9.4 - - + -
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Residues in contact with ASP 81 (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 PRO* 3.8 20.3 - - + +
77A PRO 2.8 20.9 + - - +
78A VAL* 3.2 12.0 + - + +
80A LEU* 1.3 72.6 - - - +
82A ARG* 1.3 61.4 + - + +
84A LEU 3.4 0.3 + - - -
85A ARG* 2.8 30.2 + - - +
106A GLU* 6.0 1.2 - - - +
107A ARG* 2.8 38.1 + - - +
109A TYR* 2.8 35.5 + - - -
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Residues in contact with ARG 82 (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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78A VAL* 3.1 34.1 + - + +
79A MET* 3.7 7.8 - - - +
81A ASP* 1.3 78.4 - - + +
83A VAL* 1.3 64.5 + - - +
85A ARG* 3.6 20.3 + - - +
86A LEU* 3.5 19.2 + - - +
317C ILE* 5.1 1.7 - - - +
320C ASP* 2.8 41.1 + - - +
321C ALA* 5.1 4.8 - - - +
323C MET 2.3 32.9 + - - -
324C LEU* 3.9 27.2 - - + +
329C GLY* 4.9 2.6 + - - -
330C GLY 2.8 18.1 + - - -
331C LYS* 3.5 24.8 - - - +
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Residues in contact with VAL 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ALA* 3.8 32.8 - - + +
40A ALA* 5.8 0.7 - - + -
41A ALA* 4.5 9.0 - - + +
79A MET 3.1 15.6 + - - +
80A LEU* 3.7 12.6 - - + +
82A ARG* 1.3 77.0 - - - +
84A LEU* 1.3 64.6 + - + +
86A LEU* 3.2 9.6 + - - +
87A LEU* 3.1 31.1 + - + +
146C LEU* 4.2 19.1 - - + -
150C ILE* 4.5 9.9 - - + -
321C ALA* 5.8 3.4 - - + -
324C LEU* 3.9 17.5 - - + -
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Residues in contact with LEU 84 (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 ALA* 5.7 0.7 - - + -
46A VAL* 4.2 20.2 - - + -
47A LEU* 5.3 0.9 - - + -
50A MET* 4.1 24.0 - - - -
62A PRO* 4.5 11.0 - - + -
65A ILE* 5.0 6.5 - - + -
80A LEU* 2.8 37.0 + - + +
81A ASP 3.9 0.2 - - - +
83A VAL* 1.3 74.5 - - + +
85A ARG* 1.3 57.7 + - - +
87A LEU* 3.2 13.7 + - + +
88A ALA* 2.8 31.4 + - - +
93A VAL* 3.7 21.9 - - + +
109A TYR* 3.6 41.9 - - + -
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Residues in contact with ARG 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ASP* 2.8 21.4 + - - +
82A ARG* 3.7 22.1 + - - +
83A VAL 3.3 0.2 - - - -
84A LEU* 1.3 73.7 - - - +
86A LEU* 1.3 61.9 + - - +
88A ALA* 3.4 2.4 + - - -
89A SER* 3.0 19.4 + - - -
107A ARG* 3.8 38.6 - - - +
109A TYR* 3.4 13.0 + - - +
303C LEU* 3.5 36.4 - - - +
306C SER 5.7 1.1 - - - -
307C PRO* 3.5 24.3 - - + +
317C ILE* 4.0 22.2 - - + +
320C ASP* 3.4 33.5 + - - -
332C GLU 5.3 0.4 + - - -
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Residues in contact with LEU 86 (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 VAL* 3.6 27.4 - - + +
34A LEU* 4.3 9.6 - - + -
37A ALA* 3.5 31.9 - - + -
82A ARG 3.5 8.1 + - - +
83A VAL* 3.2 10.0 + - - +
85A ARG* 1.3 76.4 - - - +
87A LEU* 1.3 65.3 + - + +
89A SER* 2.8 21.2 + - - +
90A TYR* 3.3 21.6 + - + -
317C ILE* 3.3 24.1 - - + +
318C HIS* 3.8 33.0 - - + +
321C ALA* 3.9 9.0 - - + -
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Residues in contact with LEU 87 (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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34A LEU* 3.8 25.6 - - + +
37A ALA* 4.7 4.9 - - + -
38A LEU* 4.1 35.7 - - + +
41A ALA* 4.1 25.6 - - + -
47A LEU* 5.4 2.2 - - + -
83A VAL* 3.1 20.5 + - + +
84A LEU* 3.2 20.8 + - + +
86A LEU* 1.3 76.6 - - + +
88A ALA* 1.3 61.4 + - - +
90A TYR* 3.1 4.2 + - - -
91A SER 3.1 3.5 + - - -
92A VAL* 2.9 41.2 + - + +
93A VAL* 4.0 12.6 - - + -
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Residues in contact with ALA 88 (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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84A LEU 2.8 17.1 + - - +
85A ARG 3.6 5.2 - - - +
87A LEU* 1.3 74.2 - - - +
89A SER* 1.3 67.3 + - - +
91A SER* 3.0 14.2 + - - -
93A VAL* 3.5 23.8 - - + +
95A TYR* 3.9 29.2 - - + -
109A TYR* 4.0 11.4 - - + -
307C PRO* 4.0 9.9 - - + +
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Residues in contact with SER 89 (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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85A ARG 3.0 14.2 + - - -
86A LEU* 2.8 20.5 + - - -
88A ALA* 1.3 78.5 - - - +
90A TYR* 1.3 70.2 + - - +
91A SER* 3.6 1.2 + - - -
307C PRO 3.4 14.5 + - - -
308C ASP 3.7 15.7 - - - -
309C PRO* 3.6 16.3 - - - +
314C LYS* 3.3 27.3 - - - +
317C ILE* 4.0 18.8 - - - +
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Residues in contact with TYR 90 (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 GLN* 2.9 23.3 + - - +
34A LEU* 3.7 44.4 - - + -
86A LEU* 3.3 12.1 + - + +
87A LEU 3.1 7.5 + - - +
88A ALA 3.0 1.0 - - - -
89A SER* 1.3 102.8 + - - +
91A SER* 1.3 67.7 + - - -
92A VAL* 3.2 6.7 + - + -
24C PHE* 3.4 20.8 - + + -
314C LYS* 3.5 28.6 - - + +
318C HIS* 2.6 39.9 + + - -
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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