Contacts of the helix formed by residues 86 - 102 (chain F) in PDB entry 5M64
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 THR 86 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1034A TYR* 6.0 0.2 - - + -
1180A ASN* 3.1 30.7 - - - +
1181A PRO* 5.1 8.5 - - + +
82F THR* 5.4 5.2 - - + -
84F TYR* 3.9 12.3 - - + +
85F MET* 1.3 78.4 - - - +
87F LYS* 1.3 58.5 + - - +
88F TYR* 3.4 4.2 + - - +
89F GLU* 2.8 37.8 + - + +
90F ARG* 2.9 27.8 + - - +
136F ARG* 4.5 16.2 - - - +
151F LEU* 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 87 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A ASN* 5.3 14.1 - - - +
650A LEU* 4.2 26.8 - - + +
655A SER* 5.3 11.1 + - - -
1058A THR* 5.9 1.4 + - - -
1059A LYS* 5.6 10.2 - - - +
1180A ASN* 3.4 21.6 - - + +
1183A GLU* 6.5 0.7 - - + -
85F MET 3.9 0.4 + - - -
86F THR* 1.3 72.4 - - - +
88F TYR* 1.3 75.8 + - + +
90F ARG* 3.5 10.9 - - - +
91F ALA* 3.0 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 88 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650A LEU* 3.5 39.0 - - + +
1034A TYR* 5.8 1.3 - + - +
1180A ASN* 4.0 12.3 - - - +
1181A PRO 4.8 2.2 - - - +
1182A GLY* 3.2 33.2 - - - -
1183A GLU* 3.2 32.8 - - + +
1650A GLY* 4.0 14.1 - - - +
1651A THR* 3.7 25.3 + - + -
1654A PHE* 4.7 4.3 - - + -
1082B HIS 3.5 4.5 + - - -
1083B GLY* 3.3 24.5 - - - -
86F THR* 3.3 5.1 + - - +
87F LYS* 1.3 88.6 - - + +
89F GLU* 1.3 61.8 + - + +
91F ALA* 3.5 4.6 + - + +
92F ARG* 2.9 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 89 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1034A TYR* 4.4 0.7 + - + -
1654A PHE* 3.1 52.7 - - + +
1656A VAL* 5.7 0.3 - - - +
85F MET* 4.0 12.8 - - - -
86F THR* 2.8 34.5 + - + +
88F TYR* 1.3 70.7 - - + +
90F ARG* 1.3 60.1 + - - +
92F ARG* 3.5 4.0 - - - +
93F ILE* 2.9 35.2 + - - +
134F ILE* 3.2 43.5 - - + +
136F ARG* 4.4 17.4 + - - +
151F LEU* 6.0 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 90 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A ASN* 2.3 37.9 + - - +
85F MET* 3.7 13.7 - - + +
86F THR 2.9 19.5 + - - +
87F LYS* 3.5 10.5 - - - +
88F TYR 3.2 0.4 - - - -
89F GLU* 1.3 77.2 - - - +
91F ALA* 1.3 57.7 + - - +
93F ILE* 3.2 3.2 - - - +
94F LEU* 2.8 49.9 + - + +
122F MET* 3.4 33.1 - - - +
125F LEU* 3.7 39.4 - - + +
153F VAL* 4.2 14.5 - - - +
154F ASP* 5.0 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 91 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A ASN* 3.5 12.1 - - - +
645A ALA* 4.1 7.1 - - - +
646A GLU* 4.3 30.7 - - + +
649A ASN* 4.9 9.8 + - + -
650A LEU* 5.7 4.0 - - + -
1651A THR* 6.3 1.3 - - + -
87F LYS 3.0 16.9 + - - +
88F TYR* 4.1 5.2 - - + +
90F ARG* 1.3 76.5 - - - +
92F ARG* 1.3 56.7 + - - +
94F LEU* 4.0 9.8 - - - +
95F GLY 3.0 21.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 92 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A ASN* 3.0 34.3 - - - +
1646A LEU* 5.2 4.8 - - - +
1651A THR* 3.2 27.5 + - - +
1654A PHE* 3.5 28.5 - - + -
1656A VAL* 3.6 23.1 - - + +
1086B PHE* 5.0 1.0 - - - +
88F TYR 2.9 19.5 + - - +
89F GLU* 3.5 7.6 - - - +
90F ARG 3.1 0.2 - - - -
91F ALA* 1.3 77.9 - - - +
93F ILE* 1.3 60.2 + - + +
95F GLY 3.8 0.4 - - - -
96F THR* 2.8 64.4 + - - +
99F LEU* 5.0 3.6 - - - +
109G PRO* 3.5 43.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 93 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1656A VAL* 5.3 6.1 - - + -
85F MET* 3.7 12.3 - - + -
89F GLU* 2.9 24.3 + - - +
90F ARG 3.2 6.5 - - - +
92F ARG* 1.3 77.8 - - + +
94F LEU* 1.3 67.2 + - + +
96F THR* 4.3 6.7 - - - -
97F ARG* 2.9 31.8 + - - +
121F ALA 5.5 0.9 - - - +
125F LEU* 3.7 31.4 - - + -
130F ILE* 4.3 29.3 - - + +
132F LEU* 4.8 14.1 - - + +
134F ILE* 4.0 31.0 - - + -
148F VAL* 5.4 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 94 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A ALA* 4.6 2.7 - - + +
649A ASN* 4.5 6.1 - - + +
90F ARG* 2.8 57.4 + - + +
91F ALA* 4.0 6.5 - - - +
93F ILE* 1.3 87.6 - - + +
95F GLY* 1.3 60.3 + - - +
98F ALA* 3.0 28.4 + - - +
118F LEU* 3.9 21.1 - - + +
121F ALA* 3.5 43.1 - - + +
122F MET* 3.6 21.5 - - + +
125F LEU* 4.3 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 95 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A GLU* 2.9 28.1 - - - +
642A ASN* 3.6 26.9 - - - -
645A ALA* 4.2 5.1 - - - +
91F ALA 3.0 11.4 + - - -
94F LEU* 1.3 74.8 - - - +
96F THR* 1.3 64.2 + - - +
98F ALA* 3.1 1.1 + - - -
99F LEU* 3.0 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 96 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1656A VAL* 4.5 5.4 - - + +
92F ARG* 2.8 51.4 + - - +
93F ILE* 4.3 5.2 - - - -
95F GLY* 1.3 74.7 - - - +
97F ARG* 1.3 57.4 + - - +
99F LEU* 3.2 16.3 - - + +
100F GLN* 2.9 32.2 + - + +
132F LEU* 4.2 20.4 - - + -
107G ILE* 3.9 33.7 - - + -
108G THR 5.8 0.7 - - - +
109G PRO* 6.3 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 97 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93F ILE 2.9 22.3 + - - +
94F LEU* 3.9 3.4 - - + +
96F THR* 1.3 77.4 - - - +
98F ALA* 1.3 57.3 + - - +
100F GLN* 2.8 41.0 + - - +
101F ILE* 2.8 44.1 + - + +
105F ALA* 5.7 0.2 - - - +
106F PRO 4.0 9.5 + - - -
107F VAL* 4.2 9.5 - - - +
108F PHE* 3.7 25.5 - - - -
121F ALA* 4.0 23.3 - - + +
124F GLU* 4.3 22.3 - - + +
130F ILE* 3.6 23.8 - - + +
131F PRO* 3.4 27.2 - - - +
132F LEU* 4.6 5.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 98 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A GLU* 3.2 26.5 - - + +
94F LEU 3.0 18.1 + - - +
95F GLY* 3.1 1.1 + - - -
97F ARG* 1.3 77.2 - - - +
99F LEU* 1.3 56.7 + - - +
101F ILE* 3.4 9.6 - - - +
102F SER* 3.0 32.2 + - - -
117F PRO* 3.8 30.7 - - + +
118F LEU* 4.4 5.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 99 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 4.7 9.1 - - + +
641A GLU* 3.2 26.2 + - + +
642A ASN* 4.9 7.6 - - + +
1086B PHE* 6.1 2.2 - - + -
92F ARG* 5.0 6.7 - - - +
95F GLY 3.0 17.3 + - - +
96F THR* 3.2 31.9 - - + +
98F ALA* 1.3 77.0 - - - +
100F GLN* 1.3 62.3 + - + +
102F SER* 3.0 19.2 + - - +
103F MET* 4.0 6.1 + - - +
107G ILE* 4.8 1.8 - - + -
108G THR 5.7 0.7 - - - +
109G PRO 5.0 5.8 - - - +
110G ASP 4.6 14.4 - - - +
111G THR 4.7 1.6 - - - +
112G PRO* 3.5 48.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 100 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96F THR* 2.9 23.3 + - + +
97F ARG* 2.8 45.0 + - - +
99F LEU* 1.3 83.7 - - + +
101F ILE* 1.3 69.8 + - - +
102F SER 3.6 0.2 + - - -
103F MET* 3.6 7.6 + - - +
105F ALA* 3.2 32.8 - - - +
106F PRO* 4.9 4.2 + - - +
108F PHE* 6.2 0.2 - - - -
131F PRO* 5.2 1.4 - - - +
132F LEU* 5.3 7.4 - - + +
51G PRO* 3.7 21.1 - - + +
54G LEU* 3.3 34.9 - - + +
107G ILE* 5.4 6.3 - - + -
112G PRO* 4.5 3.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 101 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A TYR* 6.1 6.0 - - + +
97F ARG* 2.8 39.5 + - + +
98F ALA* 3.4 11.7 - - - +
100F GLN* 1.3 77.6 + - - +
102F SER* 1.3 64.3 + - - +
103F MET 3.1 6.6 + - - -
104F ASN* 3.6 8.6 + - - -
105F ALA* 3.7 22.8 + - + +
107F VAL* 3.9 24.5 - - + -
111F LEU* 6.6 0.2 - - + -
117F PRO* 4.5 16.2 - - + +
120F ILE* 3.9 29.6 - - + -
121F ALA* 6.1 0.4 - - - +
124F GLU* 5.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 102 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 5.6 4.0 - - - +
509A GLU* 5.7 2.0 - - - -
510A PRO* 3.4 36.0 - - - +
512A THR* 3.7 14.5 + - - -
514A TYR* 6.3 2.7 - - - -
574A ASN* 4.5 0.3 + - - -
641A GLU* 5.6 3.1 - - - +
98F ALA 3.0 15.0 + - - -
99F LEU* 3.0 20.8 + - - -
100F GLN 3.3 0.2 - - - -
101F ILE* 1.3 78.6 - - - +
103F MET* 1.3 57.1 + - - +
104F ASN 3.4 2.0 - - - -
117F PRO* 5.0 11.7 - - - -
----------------------------------------------------------
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