Contacts of the strand formed by residues 84 - 98 (chain M) in PDB entry 1H2I
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 TRP 84 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26M PHE* 3.8 5.3 - - - -
72M ILE* 4.2 12.1 - - + -
75M ALA* 3.5 29.8 - - + -
76M ASN* 2.9 25.0 + - - +
79M PHE* 3.9 18.8 - + + -
80M GLY 3.5 15.7 - - - -
81M TYR 4.2 5.9 - - - +
82M ASN 3.6 0.2 - - - -
83M GLY* 1.3 79.5 - - - +
85M ALA* 1.3 80.2 + - - +
86M HIS* 3.8 11.9 - - + -
113M VAL* 4.0 11.2 - - + -
114M GLN 3.1 10.5 - - - +
115M LEU* 3.9 6.3 - - + -
151M LEU* 3.8 27.4 - - + -
155M LEU* 4.2 9.6 - - + -
119N SER* 4.6 3.6 - - - -
120N TYR 4.4 0.2 - - - +
121N HIS* 3.3 43.2 + + - -
157N SER* 3.8 20.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 85 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26M PHE* 3.5 19.5 - - + -
84M TRP* 1.3 80.6 - - - +
86M HIS* 1.3 61.9 + - - +
113M VAL* 3.1 8.0 - - - +
114M GLN 2.8 27.6 + - - +
120N TYR* 2.9 50.3 - - + +
121N HIS* 3.8 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 86 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84M TRP* 3.8 4.6 - - + -
85M ALA* 1.3 79.7 - - - +
87M SER* 1.3 62.4 + - - +
88M ILE* 5.4 0.4 - - + -
111M VAL* 3.9 15.7 - - + -
112M ARG 3.1 12.6 - - - +
113M VAL* 4.0 3.8 - - + -
147M VAL* 5.1 6.6 - - + +
151M LEU* 3.7 43.0 - - + +
120N TYR* 3.1 12.1 + - - -
121N HIS* 2.8 46.3 - + + -
122N GLU 3.0 45.3 + - - -
123N ASP* 4.9 6.0 + - + -
157N SER* 3.4 19.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 87 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86M HIS* 1.3 76.1 - - - +
88M ILE* 1.3 64.1 - - - +
89M THR* 3.6 6.8 + - - +
111M VAL* 3.4 6.1 - - - +
112M ARG* 2.9 42.7 + - - +
112N ARG* 5.1 6.7 - - - -
120N TYR* 3.9 18.7 + - - -
122N GLU* 3.5 18.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 88 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86M HIS* 5.4 0.2 - - + -
87M SER* 1.3 75.1 - - - +
89M THR* 1.3 62.5 + - - +
90M GLN* 3.6 27.8 - - - +
91M GLN* 4.2 5.4 - - + +
109M ALA* 5.0 3.1 - - + -
110M PHE 3.5 7.0 - - - +
111M VAL* 4.6 6.7 - - + +
147M VAL* 3.9 28.0 - - + -
110N PHE* 3.8 31.2 - - + -
122N GLU* 3.1 28.3 + - + +
123N ASP* 3.7 32.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 89 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87M SER* 3.6 6.5 + - - +
88M ILE* 1.3 74.0 - - - +
90M GLN* 1.3 63.9 + - - +
110M PHE* 2.7 24.4 + - - +
112M ARG* 4.0 27.6 - - + -
122M GLU* 2.6 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 90 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88M ILE* 3.1 8.7 - - - +
89M THR* 1.3 86.6 + - - +
91M GLN* 1.3 66.3 + - - +
92M ASN* 3.7 34.4 - - - +
109M ALA* 3.4 1.6 - - - -
110M PHE* 2.7 50.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 91 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88M ILE* 4.2 4.6 - - + +
90M GLN* 1.3 83.4 + - - +
92M ASN* 1.3 66.2 + - - +
93M VAL 4.3 0.5 + - - -
107M VAL* 3.7 17.7 - - + +
108M CYS 3.3 10.5 - - - +
109M ALA* 3.9 2.1 - - - +
143M ARG* 2.9 69.3 + - - +
146M ALA* 3.8 6.1 - - - +
147M VAL* 3.5 15.4 - - - +
110N PHE* 3.3 35.6 - - + -
124N VAL* 3.9 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 92 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143L ARG* 4.9 3.5 + - - +
90M GLN* 3.7 23.3 - - - +
91M GLN* 1.3 76.1 + - - +
93M VAL* 1.3 77.9 + - - +
94M ASP* 3.4 12.2 + - - +
107M VAL* 3.6 2.6 - - - -
108M CYS* 2.9 49.3 + - - -
110M PHE* 5.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 93 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91M GLN 4.3 0.4 + - - -
92M ASN* 1.3 80.5 + - - +
94M ASP* 1.3 63.0 + - - +
95M PHE* 3.8 13.7 - - - +
96M VAL* 3.9 25.1 - - + -
106M GLY 3.9 6.1 - - - +
107M VAL* 3.9 17.5 - - + -
139M LEU* 4.3 7.9 - - + -
143M ARG* 3.6 37.4 - - - +
94N ASP* 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 94 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93L VAL* 5.4 0.6 - - - +
139L LEU* 3.4 15.7 - - + +
143L ARG* 2.6 35.3 + - - -
92M ASN* 3.4 16.4 + - - +
93M VAL* 1.3 73.7 - - - +
95M PHE* 1.3 71.9 + - + +
106M GLY 2.7 16.8 + - - +
126M TYR* 2.6 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 95 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135L LYS* 3.7 43.5 - - + +
136L ALA* 3.4 35.0 - - + -
139L LEU* 4.0 11.9 - - + -
93M VAL* 3.4 4.8 - - - +
94M ASP* 1.3 91.0 - - + +
96M VAL* 1.3 70.9 + - - +
97M ASP* 3.5 19.7 - - - +
104M TYR* 3.4 34.8 - - + -
105M VAL* 3.4 4.4 - - - +
106M GLY* 3.3 36.7 + - - -
126M TYR* 4.0 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 96 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93M VAL* 3.9 17.3 - - + -
95M PHE* 1.3 80.9 - - - +
97M ASP* 1.3 64.9 + - - +
98M LEU 4.2 0.3 + - - -
103M PHE* 4.2 18.6 - - + -
104M TYR 3.4 3.8 - - - -
105M VAL* 4.1 13.0 - - + -
135M LYS* 4.4 23.1 - - + -
139M LEU* 3.9 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 97 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135L LYS* 2.7 35.0 + - - +
95M PHE* 3.5 13.8 - - - +
96M VAL* 1.3 81.7 + - - +
98M LEU* 1.3 60.1 + - - +
99M ASN* 3.9 19.2 - - - +
103M PHE* 3.2 9.2 - - - -
104M TYR* 2.6 54.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 98 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96M VAL 4.2 0.4 + - - -
97M ASP* 1.3 73.1 - - - +
99M ASN* 1.3 65.8 + - - +
100M ASN 3.9 19.5 - - - +
101M GLY* 4.0 12.8 - - - +
102M LYS 3.4 10.8 - - - +
103M PHE* 3.8 34.1 - - + -
----------------------------------------------------------
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