Contacts of the helix formed by residues 87 - 105 (chain A) in PDB entry 1RFT
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 ASP 87 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LEU 5.6 0.6 - - - +
58A ASN* 5.1 3.1 - - - +
59A SER* 4.4 9.4 + - - -
85A THR* 3.3 10.2 - - + +
86A ARG* 1.3 78.3 - - - +
88A LYS* 1.3 69.8 + - - +
89A SER* 2.5 36.8 + - - -
90A PHE* 3.0 32.1 + - + +
91A LEU* 3.2 17.7 + - - +
132A LEU* 4.1 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ARG 3.8 1.0 + - - -
87A ASP* 1.3 74.1 + - - +
89A SER* 1.3 68.0 + - - +
91A LEU* 3.2 6.0 + - - +
92A ALA* 3.1 21.0 + - + +
131A ASP* 3.1 45.4 + - + +
132A LEU* 3.4 25.6 - - + +
135A VAL* 4.2 16.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A SER* 3.3 27.9 + - - -
87A ASP* 2.5 20.6 + - - -
88A LYS* 1.3 82.2 - - - +
90A PHE* 1.3 59.5 + - - -
92A ALA* 3.3 9.3 - - - +
93A MET 3.3 14.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 4.1 10.5 - - + -
38A VAL* 6.0 0.2 - - + -
40A SER* 3.7 32.1 - - - -
57A LEU* 3.2 34.1 - - + -
58A ASN* 3.9 12.3 - - - -
59A SER* 4.0 7.4 - - - -
62A LEU* 3.6 41.1 - - + -
85A THR* 3.9 18.2 - - + -
87A ASP* 3.0 31.7 + - + +
89A SER* 1.3 77.6 - - - +
91A LEU* 1.3 64.8 + - - +
93A MET* 3.1 7.2 + - - +
94A VAL* 3.0 34.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A THR* 5.5 4.7 - - - +
83A GLY 5.4 1.1 - - - +
85A THR* 4.0 22.6 - - + +
87A ASP 3.2 9.5 + - - +
88A LYS* 3.5 8.1 - - - +
90A PHE* 1.3 79.0 - - - +
92A ALA* 1.3 66.1 + - - +
94A VAL* 3.1 27.5 - - + +
95A VAL* 3.1 11.1 + - - +
110A TYR* 5.4 4.5 - - - +
132A LEU* 4.7 10.8 - - + -
135A VAL* 3.7 27.8 - - + -
136A TYR* 3.9 39.0 - - + +
140A VAL* 3.6 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LYS* 3.1 11.8 + - + +
89A SER* 3.3 14.1 - - - +
90A PHE 3.1 0.2 - - - -
91A LEU* 1.3 75.5 - - - +
93A MET* 1.3 55.9 + - - +
95A VAL* 2.5 41.5 + - - +
96A ASP* 3.2 9.7 + - - +
135A VAL* 5.0 6.9 - - + +
139A LYS* 4.6 20.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A SER* 3.6 33.0 - - - +
60A ASP* 5.7 1.3 - - - +
62A LEU* 3.3 28.5 - - + -
63A GLN* 3.1 34.3 - - + +
89A SER 3.3 2.0 + - - +
90A PHE 3.1 10.9 + - - +
92A ALA* 1.3 77.4 - - - +
94A VAL* 1.3 62.6 + - - +
96A ASP* 2.9 36.2 + - - +
97A ILE* 3.0 23.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 3.9 18.8 - - + -
62A LEU* 4.0 6.3 - - + -
82A THR* 3.8 29.8 - - + -
85A THR* 5.5 2.0 - - - +
90A PHE* 3.0 38.8 - - + +
91A LEU* 3.1 21.8 - - + +
92A ALA 2.9 0.2 + - - -
93A MET* 1.3 75.8 - - - +
95A VAL* 1.3 57.9 + - + +
97A ILE* 3.7 11.1 - - - +
98A VAL* 2.8 36.9 + - + +
110A TYR* 4.6 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU 3.2 15.7 - - - +
92A ALA* 2.5 20.5 + - - +
94A VAL* 1.3 69.7 - - + +
96A ASP* 1.3 70.5 + - - +
97A ILE 3.0 1.7 + - - -
98A VAL* 3.1 5.9 + - - +
99A GLN* 2.8 46.1 + - + +
110A TYR* 6.1 2.5 - - + +
139A LYS* 4.4 19.7 - - + +
140A VAL* 3.7 30.1 - - + +
143A VAL* 4.3 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ALA* 3.9 9.6 - - - +
93A MET* 2.9 28.3 + - - +
95A VAL* 1.3 77.7 - - - +
97A ILE* 1.3 65.3 + - + +
99A GLN* 3.1 19.1 + - - +
100A GLU* 2.9 33.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 4.5 9.4 - - + -
10A ILE* 4.8 7.9 - - + -
62A LEU* 4.2 27.6 - - + -
66A TYR* 3.7 53.4 - - + -
93A MET* 3.0 22.2 + - + +
94A VAL* 3.7 12.1 - - - +
95A VAL 3.0 0.6 - - - -
96A ASP* 1.3 73.1 - - + +
98A VAL* 1.3 71.2 + - + +
99A GLN 2.9 0.7 + - - -
100A GLU* 3.1 3.7 + - - +
101A LEU* 2.8 47.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 5.9 0.9 - - + -
80A VAL* 3.8 28.5 - - + -
94A VAL* 2.8 33.7 - - + +
95A VAL* 3.1 6.6 + - - +
97A ILE* 1.3 79.1 - - + +
99A GLN* 1.3 57.0 + - + +
101A LEU* 3.5 9.4 + - - +
102A LYS* 3.0 39.6 + - + +
108A LEU* 4.7 2.7 - - + -
110A TYR* 3.9 43.7 - - + -
143A VAL* 5.0 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A VAL* 2.8 33.8 + - + +
96A ASP* 3.1 22.4 + - - +
97A ILE 2.9 0.8 + - - -
98A VAL* 1.3 72.7 - - + +
100A GLU* 1.3 69.5 + - - +
101A LEU 3.0 1.1 - - - -
102A LYS* 2.7 21.0 + - - +
103A GLN* 3.3 16.1 + - - +
143A VAL* 4.7 14.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A TYR* 3.5 37.8 + - - +
70A LYS* 3.9 18.2 + - - +
96A ASP* 2.9 19.0 + - - +
97A ILE 3.7 4.5 - - - +
99A GLN* 1.3 78.3 - - + +
101A LEU* 1.3 62.6 + - - +
103A GLN* 3.2 21.3 + - - +
104A GLN* 3.1 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 3.9 21.1 - - + -
66A TYR* 4.2 13.0 - - + +
75A ASN 3.0 29.4 - - - +
76A GLN* 4.0 1.1 - - - -
77A TYR* 3.6 33.2 - - + +
80A VAL* 4.2 9.0 - - + -
97A ILE* 2.8 38.3 + - + +
98A VAL* 3.6 6.7 - - - +
100A GLU* 1.3 78.5 - - - +
102A LYS* 1.3 56.1 + - - +
104A GLN* 3.3 8.7 - - + +
105A ASN* 3.3 18.9 + - - +
108A LEU* 3.1 18.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A VAL* 3.0 16.0 + - + +
99A GLN* 2.7 19.2 + - - +
101A LEU* 1.3 69.4 - - - +
103A GLN* 1.3 60.1 + - + +
104A GLN 3.0 1.8 - - - -
105A ASN 2.9 27.4 - - - +
106A PRO* 3.3 9.6 - - - +
108A LEU* 3.2 36.3 - - + +
110A TYR* 4.4 10.8 - - - -
143A VAL* 2.6 35.9 + - + +
145A ASP* 2.8 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A GLN* 3.7 12.3 - - - +
100A GLU* 3.6 21.2 + - - +
102A LYS* 1.3 77.5 - - + +
104A GLN* 1.3 61.2 + - - +
105A ASN* 3.5 0.9 + - - -
106A PRO* 4.9 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A TYR* 6.1 0.9 - - - +
75A ASN* 3.7 28.9 - - - +
76A GLN* 3.4 30.0 + - - +
100A GLU 3.1 12.5 + - - +
101A LEU* 3.3 17.3 - - + +
103A GLN* 1.3 81.1 - - - +
105A ASN* 1.3 59.0 + - + +
106A PRO* 4.5 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLN* 5.8 3.4 - - + -
77A TYR 3.2 30.2 + - - +
78A ASP* 3.9 13.7 + - - +
101A LEU 3.3 5.8 + - - +
102A LYS 2.9 12.5 + - - +
103A GLN 3.2 0.2 - - - -
104A GLN* 1.3 81.5 - - + +
106A PRO* 1.3 77.8 - - - +
107A ARG* 3.6 47.5 + - - +
108A LEU* 3.0 17.6 + - - +
----------------------------------------------------------
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