Contacts of the strand formed by residues 93 - 109 (chain M) in PDB entry 4FAO
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 PRO 93 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27M ILE* 4.0 24.8 - - + -
85M LEU* 4.2 16.0 - - + +
86M TYR 3.6 6.7 - - - +
87M LYS* 5.7 0.7 - - + -
91M GLY 3.6 8.5 - - - +
92M VAL* 1.3 91.4 - - + +
94M THR* 1.3 61.6 + - - +
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Residues in contact with THR 94 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85M LEU* 3.2 6.9 - - - +
86M TYR* 2.9 61.0 + - - -
88M ASP* 3.8 20.7 + - - +
92M VAL* 2.8 23.0 + - + +
93M PRO* 1.3 77.0 - - - +
95M LEU* 1.3 62.1 + - - +
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Residues in contact with LEU 95 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83M SER* 4.4 7.4 - - - -
84M VAL 3.2 26.5 - - - +
85M LEU* 4.2 12.3 - - + +
86M TYR* 4.3 2.7 - - - -
94M THR* 1.3 78.9 - - - +
96M LYS* 1.3 80.7 + - - +
97M TYR* 3.6 22.0 + - + +
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Residues in contact with LYS 96 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82M ILE 4.1 1.7 - - - +
83M SER* 3.4 1.0 - - - -
84M VAL* 2.9 40.4 + - + +
86M TYR* 3.8 17.0 - - + -
95M LEU* 1.3 79.4 + - - +
97M TYR* 1.3 79.5 + - - +
98M HIS* 3.3 44.4 - - - +
99M TYR* 4.0 19.9 - - + +
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Residues in contact with TYR 97 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81M PRO* 5.1 1.4 - - - +
82M ILE 3.4 10.6 - - - +
83M SER* 2.8 41.9 + - - -
95M LEU* 3.6 23.0 + - + +
96M LYS* 1.3 85.4 - - - +
98M HIS* 1.3 92.0 + + + +
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Residues in contact with HIS 98 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81M PRO* 4.1 21.0 - - + +
96M LYS* 3.3 22.7 - - - +
97M TYR* 1.3 110.9 - + + +
99M TYR* 1.3 57.8 + - - +
100M GLU* 3.1 34.6 + - + +
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Residues in contact with TYR 99 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17M PHE* 6.2 1.3 - + - -
22M TRP* 4.6 11.4 - + - -
25M TRP* 4.0 25.3 - + - -
26M ILE* 5.5 2.0 - - + -
81M PRO* 3.1 18.4 - - - +
82M ILE* 3.1 23.9 + - + +
84M VAL* 3.8 32.3 - - + -
96M LYS* 4.0 22.2 - - + +
97M TYR 3.6 0.2 - - - -
98M HIS* 1.3 70.4 - - - +
100M GLU* 1.3 70.0 + - - +
102M MET* 3.7 25.4 - - + +
53N LYS* 3.3 40.9 - - + +
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Residues in contact with GLU 100 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79M LEU 4.3 6.4 - - - +
81M PRO* 3.5 21.6 - - - +
98M HIS* 3.1 36.7 + - + +
99M TYR* 1.3 79.5 - - - +
101M GLY* 1.3 66.4 + - - +
102M MET* 3.9 0.3 - - - +
53N LYS* 3.6 23.2 - - - +
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Residues in contact with GLY 101 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79M LEU* 3.8 32.8 - - - +
80M SER 3.8 5.6 + - - -
99M TYR 3.7 0.8 + - - -
100M GLU* 1.3 80.8 + - - +
102M MET* 1.3 59.2 + - - +
103M SER 3.6 1.3 - - - -
52N THR* 5.6 0.4 - - - -
53N LYS* 2.8 22.9 + - - +
54N HIS* 2.8 12.8 + - - +
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Residues in contact with MET 102 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17M PHE* 4.4 12.3 - - + -
22M TRP* 4.7 3.8 - - + -
32M TYR* 2.9 56.1 + - + +
34M ALA* 3.4 7.1 - - - +
80M SER 3.2 3.6 + - - +
82M ILE* 3.8 32.1 - - + -
99M TYR* 3.7 36.8 - - + +
100M GLU 3.9 4.5 - - - +
101M GLY* 1.3 78.2 - - - +
103M SER* 1.3 60.2 + - - +
53N LYS* 3.4 28.0 - - + -
54N HIS* 3.7 11.3 - - - +
57N VAL* 4.1 15.5 - - + -
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Residues in contact with SER 103 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33M GLU 3.1 23.1 + - - -
34M ALA* 4.2 3.8 - - - +
35M TYR* 3.6 14.4 - - - -
79M LEU* 3.1 11.2 - - - +
80M SER* 3.0 42.2 + - - -
81M PRO 5.2 0.2 - - - -
82M ILE* 4.2 15.0 - - - -
101M GLY 3.6 0.4 - - - -
102M MET* 1.3 81.9 - - - +
104M VAL* 1.3 64.5 + - - +
54N HIS* 4.3 0.9 - - - -
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Residues in contact with VAL 104 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10M LYS* 3.9 20.2 + - + -
35M TYR* 3.1 46.5 - - + +
36M GLU* 4.5 0.9 - - - +
37M CYS* 4.0 14.4 - - - -
76M PRO* 4.1 18.4 - - + -
79M LEU* 3.8 4.0 - - + -
80M SER* 4.8 1.8 - - - -
103M SER* 1.3 76.2 + - - +
105M ALA* 1.3 62.1 + - - +
106M GLU 3.7 22.4 - - - +
54N HIS* 3.2 35.0 - - + +
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Residues in contact with ALA 105 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10M LYS* 3.2 23.1 + - - +
78M LYS* 2.8 46.7 + - + +
79M LEU 4.0 1.3 - - - +
80M SER* 4.1 19.3 - - - +
103M SER 3.5 1.4 + - - -
104M VAL* 1.3 73.5 - - - +
106M GLU* 1.3 66.0 - - + +
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Residues in contact with GLU 106 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10M LYS* 5.1 1.3 - - - +
76M PRO* 3.6 4.7 - - - +
77M THR* 2.8 42.4 + - - +
78M LYS* 3.3 36.4 + - + +
104M VAL* 3.7 6.7 - - - +
105M ALA* 1.3 84.6 - - + +
107M CYS* 1.3 56.5 + - - +
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Residues in contact with CYS 107 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8M CYS* 4.7 2.7 - - - -
9M GLN* 3.7 12.8 - - - -
10M LYS* 3.7 31.8 - - + +
37M CYS* 2.0 52.5 - - + -
48M ASP 4.4 9.1 - - - +
49M VAL* 5.8 1.1 - - - -
50M THR* 4.3 8.0 + - - -
74M CYS* 4.6 4.9 - - - -
75M VAL 3.5 4.9 - - - -
77M THR* 3.3 11.7 + - - +
104M VAL* 4.1 1.1 - - - -
106M GLU* 1.3 75.6 - - - +
108M GLY* 1.3 60.3 + - - +
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Residues in contact with GLY 108 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8M CYS* 4.5 4.5 - - - -
49M VAL* 3.5 20.0 - - - -
50M THR* 5.0 0.2 - - - -
74M CYS* 3.2 7.3 - - - -
75M VAL* 2.9 34.2 + - - +
77M THR* 3.4 13.2 - - - -
107M CYS* 1.3 78.3 - - - +
109M CYS* 1.3 63.3 + - - -
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Residues in contact with CYS 109 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8M CYS* 4.3 8.3 - - - -
41M CYS* 2.0 55.2 - - + -
45M LEU* 4.7 15.5 - - + -
49M VAL* 3.1 34.0 + - + +
51M PRO* 3.9 5.6 - - + +
52M THR 4.0 0.2 + - - -
55M ALA* 3.8 10.7 - - + +
72M ALA* 4.3 5.2 - - + -
73M CYS 3.4 2.2 - - - -
108M GLY* 1.3 75.2 - - - -
110M ARG* 1.3 83.2 + - - +
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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