Contacts of the strand formed by residues 84 - 91 (chain G) in PDB entry 4NQD
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 ALA 84 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G GLN* 4.0 15.0 - - + -
37G GLN 3.6 14.8 - - - +
38G HIS* 3.5 24.0 - - + +
39G ALA 5.1 2.5 - - - +
82G ASP 3.0 9.4 + - - +
83G SER* 1.3 75.2 - - - +
85G SER* 1.3 56.9 + - - +
86G TYR* 3.6 9.6 - - + -
104G LYS* 4.6 4.5 - - - -
105G LEU 2.8 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 85 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G TYR 4.0 0.2 - - - +
36G GLN* 3.6 2.6 - - - -
37G GLN* 2.8 47.3 + - - +
84G ALA* 1.3 74.2 - - - +
86G TYR* 1.3 61.1 + - - +
87G LEU* 4.1 15.2 + - - -
102G GLY* 5.2 1.5 - - - -
103G THR 3.2 6.8 + - - -
104G LYS* 3.6 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 86 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G GLN* 2.7 27.4 + - - -
20G ILE* 3.8 25.6 - - + -
34G TRP* 4.1 12.6 - - + -
35G TYR 3.4 5.8 - - - +
36G GLN* 2.9 35.0 + - + -
46G LEU* 3.8 18.6 - - + -
60G PHE* 3.8 10.2 - + - -
73G LEU* 3.5 17.9 - - + -
75G LEU* 3.7 15.3 - - + +
82G ASP* 2.9 30.8 + - - +
84G ALA* 3.6 17.7 - - + -
85G SER* 1.3 75.3 - - - +
87G LEU* 1.3 57.1 + - - +
103G THR* 2.8 29.6 + - - +
105G LEU* 3.9 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G GLN* 3.8 3.8 - - - +
33G PHE 3.8 0.5 - - - +
34G TRP* 3.5 8.2 - - - -
35G TYR* 2.9 39.7 + - + +
37G GLN* 4.0 28.0 - - + +
43G PRO* 4.2 22.7 - - + -
85G SER* 4.5 12.1 - - - -
86G TYR* 1.3 75.4 - - - +
88G CYS* 1.3 58.7 + - - +
99G TRP* 4.1 31.9 - - + -
100G GLY 4.8 4.7 - - - +
101G ALA 4.8 3.4 - - - +
102G GLY* 3.7 22.2 - - - +
37H GLN* 4.4 11.7 - - - +
43H LEU* 4.5 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 88 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G ILE* 4.0 4.0 - - + +
6G GLN* 3.0 21.3 + - - +
22G CYS* 2.0 54.1 - - + -
32G LEU* 3.8 24.0 - - - -
33G PHE 3.6 3.8 - - - -
34G TRP* 4.1 7.6 - - + -
87G LEU* 1.3 72.3 - - - +
89G ALA* 1.3 62.0 - - - +
99G TRP* 3.7 1.7 - - - -
100G GLY 2.7 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 89 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G ILE* 5.1 0.2 - - - -
32G LEU* 3.4 3.5 - - - +
33G PHE* 2.8 43.3 + - + +
35G TYR* 4.9 0.2 - - + -
88G CYS* 1.3 75.5 - - - +
90G VAL* 1.3 65.4 + - - +
97G LEU* 3.7 21.3 - - + -
98G ILE 3.3 7.2 - - - +
99G TRP* 3.5 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 90 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G ILE* 3.8 16.6 - - + -
24G TYR* 3.8 20.6 - - + -
26G THR* 3.9 21.5 - - + +
29G PHE* 3.7 21.8 - - + -
31G GLY 3.4 3.6 - - - +
32G LEU* 3.6 33.4 - - + -
89G ALA* 1.3 75.3 - - - +
91G LYS* 1.3 72.9 + - - +
96G GLN 3.3 2.9 - - - +
97G LEU* 3.4 4.9 - - - -
98G ILE* 2.8 39.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 91 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G PHE* 3.6 4.0 - - - -
30G ASN* 2.7 41.6 + - + -
31G GLY 3.0 12.8 + - - +
33G PHE* 3.6 11.5 - - + -
90G VAL* 1.3 73.8 - - - +
92G ASP* 1.3 59.7 + - - +
95G TYR* 4.0 28.3 - - + +
96G GLN 3.5 2.9 - - - -
97G LEU* 3.7 26.2 - - + +
97H THR* 5.9 6.1 - - - +
98H GLY 6.3 0.2 - - - +
99H GLU 3.0 16.0 + - - +
100H GLY* 2.7 36.3 + - - +
102H GLY 2.9 26.1 + - - -
----------------------------------------------------------
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