Contacts of the strand formed by residues 81 - 91 (chain H) in PDB entry 4ZMA
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 GLN 81 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66H ALA 3.6 1.9 - - - +
67H VAL* 3.5 1.7 - - - -
68H LEU* 2.7 45.5 + - + +
79H ASP 4.0 7.7 + - - +
80H GLU* 1.3 79.5 - - - +
82H SER* 1.3 63.0 + - - +
83H ARG* 4.0 19.5 + - - +
112H VAL* 3.7 9.3 - - + +
113H VAL* 3.0 49.0 + - - +
115H THR* 3.7 14.5 + - - +
118H VAL* 3.6 18.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 82 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65H ILE* 4.0 14.8 - - - +
66H ALA 3.6 4.5 - - - -
67H VAL* 3.8 20.6 - - - +
80H GLU* 4.2 3.0 - - - +
81H GLN* 1.3 72.6 + - - +
83H ARG* 1.3 81.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 83 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65H ILE* 3.4 5.9 - - - +
66H ALA* 2.8 42.0 + - - +
81H GLN* 4.0 16.9 + - - +
82H SER* 1.3 99.6 + - - +
84H ARG* 1.3 62.4 + - - +
108H LEU* 4.2 22.0 - - + -
109H HIS* 5.0 0.7 - - - +
110H GLN* 3.3 35.9 + - - +
111H PRO 3.3 18.2 + - - -
112H VAL* 3.4 34.2 - - + +
113H VAL* 4.1 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 84 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62H ARG 5.3 8.5 - - - +
64H LEU 3.7 8.5 - - - +
65H ILE* 4.6 9.2 - - + +
83H ARG* 1.3 73.5 - - - +
85H VAL* 1.3 60.5 + - - +
86H ALA 3.3 0.7 + - - -
108H LEU* 3.6 3.4 - - - -
109H HIS* 2.8 51.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 85 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H LEU* 4.4 1.6 - - + -
61H TRP 4.5 7.6 - - - +
64H LEU* 3.0 40.7 + - + +
65H ILE 4.3 0.4 - - - -
66H ALA* 4.1 22.4 - - + +
84H ARG* 1.3 71.2 - - - +
86H ALA* 1.3 64.2 + - - +
87H GLN 4.1 7.2 - - - +
88H VAL* 3.6 30.5 - - + -
106H LEU* 4.0 31.0 - - + -
107H ARG 3.8 3.8 - - - +
108H LEU* 4.6 3.8 - - + +
250H VAL* 4.4 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 86 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84H ARG* 3.3 4.0 + - - -
85H VAL* 1.3 72.8 - - - +
87H GLN* 1.3 60.4 + - + +
107H ARG* 2.7 29.8 + - - +
108H LEU 4.3 0.9 - - - -
109H HIS* 3.8 32.3 - - + +
248H PRO 5.2 2.4 - - - +
249H GLY 4.8 0.9 - - - +
250H VAL* 4.0 18.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 87 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85H VAL* 3.4 1.4 - - - +
86H ALA* 1.3 82.5 - - + +
88H VAL* 1.3 62.5 + - - +
89H ILE* 3.8 19.5 - - + +
105H LEU 3.5 2.8 - - - +
106H LEU* 3.4 3.3 - - - -
107H ARG* 2.8 68.3 + - + +
246H PRO* 3.6 9.8 - - + +
247H ARG* 2.8 42.6 + - - +
249H GLY 3.1 12.5 + - - -
250H VAL* 3.4 13.9 - - - +
252H LEU* 3.9 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 88 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H PHE* 4.1 32.5 - - + -
61H TRP* 4.1 18.6 - - + -
64H LEU* 3.6 18.6 - - + -
85H VAL* 3.6 24.5 - - + -
87H GLN* 1.3 72.0 - - - +
89H ILE* 1.3 63.5 + - - +
90H ILE* 4.2 7.0 - - + -
104H ALA* 4.4 6.1 - - + -
105H LEU 3.8 2.5 - - - -
106H LEU* 4.2 12.8 - - + +
250H VAL* 2.9 15.6 + - + +
251H LEU* 3.4 7.4 - - + +
252H LEU* 2.9 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 89 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51H TRP* 4.0 29.6 - - + -
87H GLN* 3.8 30.3 - - + +
88H VAL* 1.3 76.9 - - - +
90H ILE* 1.3 62.4 + - - +
104H ALA* 3.3 3.5 - - - -
105H LEU* 2.7 50.3 + - + +
107H ARG* 4.9 1.8 - - - +
237H TRP* 4.0 3.3 - - + -
241H LEU* 3.7 39.0 - - + +
244H SER* 5.3 1.6 - - - +
252H LEU* 3.3 25.4 - - + +
254H ALA* 3.7 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 90 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H ALA* 4.1 13.2 - - + +
59H PHE* 5.3 4.3 - - + -
88H VAL* 4.6 9.0 - - + -
89H ILE* 1.3 79.3 - - - +
91H PRO* 1.3 73.8 - - + +
94H TYR* 4.0 25.4 - - + +
96H PRO* 6.2 1.8 - - + -
103H ILE 3.6 4.9 - - - +
104H ALA* 3.5 23.1 - - + -
237H TRP* 3.8 5.2 - - - -
251H LEU* 3.9 26.0 - - + -
252H LEU 3.2 2.6 + - - +
253H ARG* 3.3 23.3 - - + +
254H ALA* 2.9 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 91 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90H ILE* 1.3 94.7 - - + +
92H SER* 1.3 63.9 + - - +
93H THR* 3.5 19.7 - - - +
94H TYR* 3.1 23.0 + - + +
101H HIS* 4.0 14.1 - - + +
103H ILE* 3.1 38.6 - - + +
234H TYR* 4.5 6.3 - - + -
237H TRP* 3.6 18.8 - - + -
253H ARG* 4.9 1.8 - - - +
254H ALA 3.4 5.6 - - - +
256H PHE* 4.0 13.2 - - + -
----------------------------------------------------------
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