Contacts of the strand formed by residues 93 - 109 (chain G) 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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G ILE* 4.0 23.1 - - + -
85G LEU* 4.0 14.4 - - + -
86G TYR 3.6 7.2 - - - +
87G LYS* 4.7 1.3 - - + -
91G GLY 3.6 8.3 - - - +
92G VAL* 1.3 87.5 - - + +
94G THR* 1.3 60.0 + - - +
17K ASN* 5.4 0.2 - - - +
21K GLU* 3.7 1.4 - - - +
46K ARG* 4.1 22.7 - - - +
55K VAL* 4.1 27.0 - - + +
56K LYS* 3.1 22.4 + - + -
81K VAL* 4.5 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 94 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85G LEU* 3.1 7.0 - - - +
86G TYR* 2.9 65.7 + - - -
88G ASP* 3.8 19.5 + - - +
92G VAL* 3.1 16.8 + - + +
93G PRO* 1.3 75.5 - - - +
95G LEU* 1.3 62.5 + - - +
21K GLU* 3.4 27.4 - - + +
56K LYS* 4.1 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83G SER* 4.4 2.5 - - - -
84G VAL 3.1 26.5 - - - +
85G LEU* 4.3 7.0 - - + +
86G TYR* 4.3 2.7 - - - -
94G THR* 1.3 78.7 - - - +
96G LYS* 1.3 78.7 + - - +
97G TYR* 3.5 20.5 + - + +
13K TYR* 6.6 0.2 - - + -
21K GLU* 5.7 0.2 + - - -
42K TYR* 3.5 36.6 - - + +
56K LYS* 4.6 8.1 - - - +
59K CYS 4.3 8.5 - - - +
60K TRP* 4.2 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 96 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82G ILE 4.0 1.6 - - - +
83G SER* 3.4 0.9 - - - -
84G VAL* 2.9 40.7 + - + +
86G TYR* 3.9 16.4 - - + -
95G LEU* 1.3 80.6 + - - +
97G TYR* 1.3 80.3 + - - +
98G HIS* 3.3 45.7 - - - +
99G TYR* 3.9 20.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 97 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82G ILE 3.4 6.2 - - - +
83G SER* 2.7 35.9 + - - -
95G LEU* 3.5 17.4 + - + +
96G LYS* 1.3 86.3 - - - +
98G HIS* 1.3 85.3 + + + +
29K GLU* 6.0 3.6 - - - -
31K CYS* 4.1 5.2 - - - +
32K GLU* 2.5 44.0 + - + -
39K LEU* 4.0 5.7 - - - +
59K CYS* 3.8 22.8 - - + +
60K TRP 3.8 18.7 + - - -
61K LEU* 3.2 41.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 98 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81G PRO* 4.1 17.8 - - + +
96G LYS* 3.3 24.3 - - - +
97G TYR* 1.3 106.9 - + + +
99G TYR* 1.3 58.9 + - - +
100G GLU* 3.1 36.1 + - - +
32K GLU* 4.6 11.3 + - + +
33K GLY* 5.6 2.8 - - - -
61K LEU* 4.1 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 99 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G PHE* 6.2 1.1 - + - -
22G TRP* 4.4 9.5 - + - -
25G TRP* 4.0 17.6 - + - -
26G ILE* 5.4 1.8 - - + -
81G PRO* 3.1 16.8 - - - +
82G ILE* 3.0 24.6 + - + +
84G VAL* 3.9 31.9 - - + -
96G LYS* 3.9 23.5 - - + +
97G TYR 3.5 0.6 - - - -
98G HIS* 1.3 71.2 - - - +
100G GLU* 1.3 68.9 + - - +
102G MET* 3.6 31.1 - - + +
53H LYS* 4.0 20.0 - - + +
75J GLU* 2.4 40.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 100 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79G LEU 4.2 6.2 - - - +
81G PRO* 3.4 21.9 - - - +
98G HIS* 3.1 37.5 + - + +
99G TYR* 1.3 78.3 - - - +
101G GLY* 1.3 66.5 + - - +
102G MET* 3.9 1.6 - - - +
53H LYS* 3.6 22.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 101 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79G LEU* 3.8 25.6 - - - +
80G SER 3.7 10.7 + - - -
99G TYR 3.6 1.2 + - - -
100G GLU* 1.3 81.0 + - - +
102G MET* 1.3 59.3 + - - +
103G SER 3.6 1.6 - - - -
52H THR* 5.9 0.2 - - - -
53H LYS* 3.3 5.4 + - - +
54H HIS* 2.8 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 102 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G PHE* 4.3 12.8 - - + -
22G TRP* 4.7 3.1 - - + -
32G TYR* 2.8 56.7 + - + +
34G ALA* 3.3 7.1 - - - +
80G SER 3.1 3.8 + - - +
82G ILE* 3.8 28.7 - - + -
99G TYR* 3.6 46.4 - - + +
100G GLU 3.9 4.0 - - - +
101G GLY* 1.3 79.7 - - - +
103G SER* 1.3 59.0 + - - +
53H LYS* 4.2 19.5 - - - -
54H HIS* 3.5 11.7 - - - +
57H VAL* 4.2 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 103 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G GLU 3.1 23.0 + - - -
34G ALA* 4.2 3.8 - - - +
35G TYR* 3.6 14.0 - - - -
79G LEU* 3.0 17.1 - - - +
80G SER* 3.0 35.9 + - - -
82G ILE* 4.2 15.7 - - - -
101G GLY 3.6 0.4 - - - -
102G MET* 1.3 82.2 - - - +
104G VAL* 1.3 64.1 + - - +
54H HIS* 4.2 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 104 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G LYS* 3.8 15.5 + - + -
35G TYR* 3.1 48.3 - - + +
36G GLU* 4.4 0.7 - - - +
37G CYS* 3.9 19.5 - - - -
76G PRO* 4.1 18.2 - - + -
79G LEU* 3.7 3.8 - - - -
80G SER* 4.8 1.6 - - - -
103G SER* 1.3 76.9 + - - +
105G ALA* 1.3 64.1 + - - +
106G GLU 3.7 22.2 - - - +
54H HIS* 3.4 31.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 105 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G LYS* 3.2 24.4 + - - +
78G LYS* 2.7 35.6 + - + +
79G LEU 3.9 2.5 - - - +
80G SER* 4.0 20.0 - - - +
103G SER 3.5 1.0 + - - -
104G VAL* 1.3 72.7 - - - +
106G GLU* 1.3 67.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 106 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G LYS* 5.1 1.3 - - - +
50G THR* 5.6 1.7 + - - -
76G PRO* 3.7 5.0 - - - +
77G THR* 2.8 37.7 + - - +
78G LYS* 3.4 21.1 + - + +
104G VAL* 3.7 6.8 - - - +
105G ALA* 1.3 86.4 - - + +
107G CYS* 1.3 59.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 107 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G CYS* 4.8 1.6 - - - -
9G GLN* 3.7 22.7 - - - -
10G LYS* 3.7 23.6 - - + +
37G CYS* 2.0 51.6 - - + -
48G ASP 4.4 9.9 - - - +
49G VAL* 5.3 0.7 - - - -
50G THR* 4.3 8.5 + - - -
74G CYS* 4.6 5.8 - - - -
75G VAL 3.6 3.4 - - - -
77G THR* 3.3 12.3 + - - +
104G VAL* 4.1 1.1 - - - -
106G GLU* 1.3 75.1 - - - +
108G GLY* 1.3 59.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 108 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G CYS* 4.5 4.3 - - - -
49G VAL* 3.4 19.3 - - - -
73G CYS 3.3 0.3 - - - +
74G CYS* 3.2 6.4 - - - -
75G VAL* 2.9 35.8 + - - +
77G THR* 3.4 13.9 - - - -
107G CYS* 1.3 78.9 - - - +
109G CYS* 1.3 62.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 109 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G CYS* 4.3 7.9 - - - -
41G CYS* 2.0 56.1 - - + -
45G LEU* 4.8 14.4 - - + -
49G VAL* 3.1 33.5 + - + +
51G PRO* 4.0 4.5 - - + +
52G THR 4.0 0.2 + - - -
55G ALA* 3.8 11.5 - - + +
72G ALA* 4.3 5.4 - - + -
73G CYS 3.4 2.2 - - - -
108G GLY* 1.3 73.7 - - - -
110G ARG* 1.3 83.6 + - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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