Contacts of the strand formed by residues 94 - 102 (chain G) in PDB entry 3CHB
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 ARG 94 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G GLN* 4.8 6.6 + - - +
18G HIS* 4.8 3.6 - - + +
47G THR 4.1 5.7 + - - +
48G PHE* 3.3 31.0 - - + +
49G GLN 2.9 23.9 + - - -
87G VAL* 3.9 16.6 - - + -
88G TRP 3.6 5.4 - - - +
89G ASN* 3.9 20.8 + - - +
91G LYS 2.9 21.1 + - - -
92G THR* 3.2 10.3 + - - +
93G PRO* 1.3 72.0 - - - +
95G ALA* 1.3 58.9 + - - +
6001G MES 2.9 46.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G GLN* 3.5 8.5 - - + +
51G GLU* 3.6 39.7 - - + +
87G VAL* 3.1 3.4 - - - -
88G TRP* 2.8 48.6 + - + -
91G LYS* 4.2 13.7 - - + -
93G PRO 3.3 0.2 + - - -
94G ARG* 1.3 71.8 - - - +
96G ILE* 1.3 64.5 + - - +
97G ALA 3.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 96 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G ILE* 4.0 13.2 - - + -
48G PHE* 3.8 28.9 - - + -
49G GLN 2.8 22.4 + - - +
50G VAL* 4.3 8.5 - - + +
51G GLU 5.7 0.7 + - - -
68G MET* 4.0 24.7 - - + -
72G LEU* 3.7 30.5 - - + -
85G LEU* 4.4 13.9 - - + -
86G CYS 3.8 3.8 - - - +
87G VAL* 4.3 2.9 - - + -
88G TRP* 3.5 4.7 - - - -
95G ALA* 1.3 70.4 - - - +
97G ALA* 1.3 60.4 + - - +
98G ALA 3.7 21.8 - - - +
31H LEU* 3.4 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 97 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G LEU* 5.7 0.4 - - + -
12G TYR* 6.3 0.7 - - + -
15G THR* 5.3 0.9 - - + -
86G CYS* 2.8 32.3 + - - +
87G VAL* 4.7 0.4 - - - +
88G TRP* 3.5 38.1 - - + -
95G ALA 3.4 1.2 + - - -
96G ILE* 1.3 75.2 - - - +
98G ALA* 1.3 60.0 + - + +
30H SER* 3.5 1.4 + - - -
31H LEU* 2.8 31.1 + - - +
32H ALA* 3.6 10.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 98 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G ILE* 3.7 21.8 - - + -
8G LEU* 4.3 9.4 - - + -
68G MET* 4.0 2.9 - - - -
85G LEU* 3.5 8.0 - - - +
86G CYS* 2.9 33.3 + - + +
96G ILE* 3.7 5.3 - - - +
97G ALA* 1.3 80.4 - - - +
99G ILE* 1.3 62.2 + - - +
28H THR* 5.1 1.6 - - + -
29H GLU 3.2 14.8 - - - +
30H SER* 3.8 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 99 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G ILE* 3.6 4.0 - - - -
24G ILE* 5.4 0.7 - - + -
40G ILE* 6.0 0.2 - - + -
68G MET* 3.7 22.9 - - + -
71G THR* 4.3 15.0 - - + -
72G LEU* 3.7 26.0 - - + -
75G ALA* 5.5 1.6 - - + -
82G VAL* 4.0 21.8 - - + -
84G LYS 3.5 4.7 - - - +
85G LEU* 3.7 18.4 - - + -
98G ALA* 1.3 76.3 - - - +
100G SER* 1.3 73.2 + - - +
101G MET* 4.5 13.7 - - + -
27H TYR* 5.7 1.3 - - + +
28H THR* 3.2 5.4 - - - +
29H GLU* 2.9 45.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 100 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G ILE* 3.6 12.5 - - - +
82G VAL* 3.7 6.1 - - - +
83G GLU* 2.6 53.9 + - - -
84G LYS* 2.9 31.8 + - - +
99G ILE* 1.3 74.8 - - - +
101G MET* 1.3 58.2 + - - +
26H SER* 5.9 2.0 - - - -
27H TYR 3.4 4.9 - - - -
28H THR* 3.4 19.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 101 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G THR* 4.2 18.8 - - + -
75G ALA* 4.0 26.2 - - + -
80G ALA* 4.1 15.9 - - - +
81G LYS 3.5 15.7 - - - +
82G VAL* 4.5 3.1 - - - -
83G GLU* 4.0 0.9 - - - +
99G ILE* 4.5 14.6 - - + -
100G SER* 1.3 77.6 - - - +
102G ALA* 1.3 60.0 + - - +
26H SER* 3.1 8.2 - - - -
27H TYR* 2.8 58.5 + - + +
73H ARG* 4.8 4.7 - - + -
76H TYR* 3.3 26.6 + - + -
77H LEU* 4.3 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 102 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G ASN* 5.2 0.7 - - - +
81G LYS* 3.3 24.8 + - - +
83G GLU* 4.1 26.8 - - + +
101G MET* 1.3 75.5 - - - +
103G ASN* 1.3 71.4 + - - +
25H PHE* 3.8 24.5 - - + +
26H SER* 3.9 10.1 - - - -
76H TYR* 3.1 8.8 + - - -
----------------------------------------------------------
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