Contacts of the strand formed by residues 91 - 102 (chain H) in PDB entry 3AOI
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 91 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76H PRO* 4.1 2.8 - - - +
77H PRO* 3.2 23.8 - - - +
88H LEU* 5.6 1.0 - - - +
89H THR* 2.7 46.9 + - - +
90H TYR* 1.3 73.8 - - - +
92H ALA* 1.3 56.5 + - - +
117H HIS* 2.8 52.7 + - + +
118H ILE 2.8 26.2 - - - +
119H PRO* 3.4 7.9 - - + -
120H LEU* 4.0 4.5 - - - -
379H GLU* 4.3 8.7 + - - -
383H ARG* 5.5 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 92 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73H LEU* 3.7 26.0 - - + -
74H GLY* 4.7 1.8 - - - +
76H PRO* 4.7 3.6 - - + -
91H GLN* 1.3 69.3 - - - +
93H PRO* 1.3 71.3 - - + +
117H HIS* 3.3 4.4 - - - -
118H ILE* 2.4 50.1 + - + +
120H LEU* 3.4 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 93 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73H LEU* 2.7 31.5 - - - +
74H GLY 4.0 1.3 - - - +
75H GLU* 2.9 53.4 - - + +
76H PRO 3.9 0.2 - - - -
77H PRO* 3.9 6.1 - - + -
92H ALA* 1.3 84.4 - - + +
94H LEU* 1.3 53.2 + - - +
95H TYR* 4.3 21.3 - - + +
114H PHE* 6.5 0.2 - - + -
116H GLY 4.4 1.1 - - - +
117H HIS* 4.2 19.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 94 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44H ILE* 5.7 3.1 - - + -
48H PHE* 5.0 13.5 - - + -
71H TYR* 5.0 5.6 - - + -
72H ARG 4.5 1.6 - - - +
73H LEU* 3.7 10.5 - - + -
92H ALA 3.5 0.2 + - - -
93H PRO* 1.3 74.8 - - - +
95H TYR* 1.3 82.4 + - - +
114H PHE* 3.8 1.9 - - - +
115H LEU* 3.0 37.6 + - + +
116H GLY 3.3 16.4 + - - +
118H ILE* 3.7 38.8 - - + -
344H PHE* 3.7 31.4 - - + -
378H LEU* 3.9 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 95 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72H ARG* 2.8 94.3 + - + +
73H LEU* 4.3 6.7 - - - -
74H GLY 5.7 0.3 + - - -
75H GLU* 5.2 6.2 + - - +
93H PRO* 4.6 23.2 - - + +
94H LEU* 1.3 83.4 - - - +
96H ALA* 1.3 65.1 + - - +
112H GLU* 3.8 20.4 - - + -
113H VAL 3.4 16.4 - - - +
114H PHE* 3.4 25.6 - - + -
115H LEU* 3.5 8.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 96 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H PHE* 3.8 24.9 - - + -
68H PHE* 4.2 4.3 - - + -
70H GLU 3.1 19.3 - - - +
71H TYR* 3.5 9.4 - - + +
72H ARG* 4.4 2.7 - - - +
95H TYR* 1.3 82.2 - - - +
97H ARG* 1.3 54.0 + - - +
98H LEU* 2.7 32.7 - - + +
112H GLU* 4.2 6.9 - - - +
113H VAL 3.7 11.9 + - - +
115H LEU* 4.0 3.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 97 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68H PHE* 4.2 3.8 - - - -
69H LEU* 2.8 49.0 + - + +
70H GLU* 2.9 36.9 + - - +
72H ARG* 5.0 15.8 - - - +
96H ALA* 1.3 73.0 - - - +
98H LEU* 1.3 58.7 + - - +
110H GLU* 3.8 28.0 + - + -
111H ASP* 3.4 17.7 - - - +
112H GLU* 4.6 12.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 98 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H PHE* 6.2 0.7 - - + -
52H PHE* 3.4 28.5 - - + -
66H LEU* 3.6 17.7 - - + +
67H ASP 3.4 5.2 - - - -
69H LEU* 3.7 2.5 - - - -
96H ALA* 2.7 26.5 - - + +
97H ARG* 1.3 75.8 - - - +
99H GLN* 1.3 60.1 + - - +
109H LYS 3.6 1.7 - - - +
111H ASP 3.1 37.3 + - - +
113H VAL* 3.5 33.0 - - + +
115H LEU* 5.9 3.1 - - + -
351H LEU* 6.1 1.3 - - + -
369H PRO* 4.7 9.4 - - + +
373H VAL* 3.8 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 99 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65H VAL 3.7 1.0 - - - +
66H LEU* 3.3 3.5 - - - -
67H ASP* 2.7 46.4 + - + +
69H LEU* 3.2 34.6 - - + +
98H LEU* 1.3 75.2 - - - +
100H LEU* 1.3 56.6 + - - +
101H ILE* 3.0 27.0 + - + +
108H ILE* 3.9 12.7 - - + +
109H LYS 2.8 16.2 - - - +
110H GLU* 4.0 9.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 100 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64H LEU* 3.3 28.5 - - + -
65H VAL 2.8 29.6 - - - +
66H LEU* 3.9 11.8 - - + +
99H GLN* 1.3 72.1 - - - +
101H ILE* 1.3 68.7 + - - +
102H HIS* 3.5 28.2 + - + +
108H ILE* 3.2 4.2 - - - -
109H LYS* 2.7 40.8 + - + +
367H LEU* 3.5 34.3 - - + +
368H THR* 5.1 4.3 - - - -
369H PRO* 6.1 2.5 - - + -
372H LEU* 3.9 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 101 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63H GLY 4.5 1.7 - - - +
64H LEU 4.5 0.3 - - - -
65H VAL* 2.5 53.8 + - + +
67H ASP* 4.9 5.8 - - - +
99H GLN* 3.0 40.6 - - + +
100H LEU* 1.3 82.9 - - - +
102H HIS* 1.3 71.8 + - - +
105H THR* 5.2 4.7 - - - +
107H LEU 4.3 0.7 - - - +
108H ILE* 3.0 41.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 102 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63H GLY 4.7 2.0 - - - -
65H VAL* 5.9 2.0 - - - -
100H LEU* 3.5 41.7 + - + +
101H ILE* 1.3 83.3 + - - +
103H LYS* 1.3 64.5 - - - +
104H ASP* 2.8 34.0 + - + +
105H THR* 3.3 7.3 + - - +
107H LEU* 3.0 46.6 + - + +
108H ILE* 3.7 7.6 - - - -
109H LYS* 4.4 13.1 + - + +
359H MET* 6.3 0.8 - - - +
364H GLU* 5.3 7.1 + - - +
365H ASP* 5.0 14.9 + - + +
367H LEU* 4.8 8.5 - - + -
----------------------------------------------------------
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