Contacts of the helix formed by residues 87 - 105 (chain D) in PDB entry 1RFU
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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A PRO* 5.1 16.2 - - + +
56D VAL* 5.1 5.2 - - + -
57D LEU 3.7 10.1 - - - +
58D ASN* 3.4 27.2 - - - +
85D THR* 3.2 5.7 - - + +
86D ARG* 1.3 80.4 - - - +
88D LYS* 1.3 58.4 + - - +
89D SER* 2.5 44.7 + - - -
90D PHE* 3.0 22.0 + - + +
91D LEU 2.8 24.4 + - - -
132D LEU* 3.7 4.1 - - - +
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Residues in contact with LYS 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D ARG 3.9 2.2 + - - -
87D ASP* 1.3 69.3 + - - +
89D SER* 1.3 76.5 + - - +
91D LEU* 3.3 1.4 + - - +
92D ALA* 2.8 27.4 + - + +
131D ASP* 3.7 40.5 + - + +
132D LEU* 3.3 19.8 - - + +
135D VAL* 3.6 19.0 - - + +
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Residues in contact with SER 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D SER* 2.8 30.8 + - - -
87D ASP* 2.5 22.6 + - - -
88D LYS* 1.3 85.5 + - - +
90D PHE* 1.3 59.7 + - - -
92D ALA* 3.2 6.5 + - - +
93D MET* 3.0 25.1 + - - +
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Residues in contact with PHE 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ILE* 3.6 26.9 - - + -
38D VAL* 4.4 3.6 - - + -
40D SER* 3.5 27.8 - - - -
57D LEU* 3.8 35.9 - - + -
58D ASN 4.2 3.6 - - - -
59D SER* 4.3 6.5 + - - +
62D LEU* 3.3 43.5 - - + +
85D THR* 3.2 30.1 - - + -
87D ASP* 2.9 25.4 + - + +
89D SER* 1.3 77.6 - - - +
91D LEU* 1.3 63.0 + - - +
93D MET* 3.3 3.2 + - - +
94D VAL* 3.0 31.1 + - + +
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Residues in contact with LEU 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D THR* 5.7 4.3 - - - +
83D GLY 5.7 0.2 - - - +
85D THR* 5.0 9.0 - - + +
87D ASP 2.8 15.4 + - - +
88D LYS 3.6 6.5 - - - +
90D PHE* 1.3 75.9 - - - +
92D ALA* 1.3 65.0 + - - +
94D VAL* 3.1 30.1 + - + +
95D VAL* 3.2 6.2 + - - +
110D TYR* 5.5 1.8 - - - +
132D LEU* 3.7 11.7 - - + -
135D VAL* 3.4 26.9 - - + -
136D TYR* 3.3 56.5 - - + +
140D VAL* 3.7 18.4 - - + -
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Residues in contact with ALA 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D LYS* 2.8 23.8 + - + +
89D SER* 3.4 7.9 - - - +
91D LEU* 1.3 72.3 - - - +
93D MET* 1.3 54.0 + - - +
95D VAL* 2.7 35.3 + - - +
96D ASP* 3.3 9.0 + - - +
135D VAL* 4.0 14.3 - - + +
139D LYS* 4.1 20.1 + - - +
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Residues in contact with MET 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D SER* 3.2 37.0 - - - +
62D LEU* 4.0 13.7 - - + -
63D GLN* 2.5 46.4 - - + +
89D SER 3.0 13.8 + - - +
90D PHE* 3.6 4.3 - - - +
92D ALA* 1.3 74.8 - - - +
94D VAL* 1.3 69.1 + - - +
96D ASP* 2.9 17.9 + - + +
97D ILE* 2.9 31.5 + - + +
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Residues in contact with VAL 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ILE* 4.2 16.2 - - + -
62D LEU* 3.8 17.3 - - + -
82D THR* 3.7 31.9 - - + -
85D THR* 5.6 0.4 - - - +
90D PHE* 3.0 39.4 + - + +
91D LEU* 3.1 17.5 + - + +
93D MET* 1.3 75.7 - - - +
95D VAL* 1.3 58.2 + - + +
97D ILE* 3.2 10.1 + - + +
98D VAL* 2.8 41.7 + - + +
110D TYR* 4.6 4.5 - - - +
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Residues in contact with VAL 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D LEU* 3.6 5.8 - - + +
92D ALA* 2.7 17.6 + - - +
94D VAL* 1.3 78.4 - - + +
96D ASP* 1.3 66.2 + - - +
98D VAL* 2.9 20.7 + - + +
99D GLN* 2.9 32.0 + - - +
110D TYR* 5.8 0.7 - - + +
139D LYS* 3.7 37.2 - - + +
140D VAL* 3.5 34.8 - - + -
143D VAL* 4.3 9.9 - - + -
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Residues in contact with ASP 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D ALA 3.3 6.2 + - - +
93D MET* 2.9 18.0 + - + +
95D VAL* 1.3 74.9 - - - +
97D ILE* 1.3 64.3 + - + +
99D GLN* 3.1 13.9 + - - +
100D GLU* 2.9 23.5 + - - +
139D LYS* 3.2 26.4 + - - -
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Residues in contact with ILE 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D LEU* 4.7 8.5 - - + -
10D ILE* 5.3 6.3 - - + -
62D LEU* 4.1 29.8 - - + -
63D GLN* 6.2 0.2 - - - +
66D TYR* 3.6 61.0 - - + -
93D MET* 2.9 26.9 + - + +
94D VAL* 3.3 9.2 - - - +
96D ASP* 1.3 75.9 - - + +
98D VAL* 1.3 66.3 + - + +
100D GLU* 3.0 9.5 + - - +
101D LEU* 3.0 36.6 + - + +
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Residues in contact with VAL 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D VAL* 4.3 15.3 - - + -
94D VAL* 2.8 48.0 + - + +
95D VAL* 3.2 10.3 - - - +
97D ILE* 1.3 72.2 - - + +
99D GLN* 1.3 60.6 + - + +
101D LEU* 3.2 12.7 + - - +
102D LYS* 2.8 32.9 + - + +
108D LEU* 5.0 3.7 - - + +
110D TYR* 3.5 44.9 - - + -
143D VAL* 4.3 13.7 - - + -
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Residues in contact with GLN 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D VAL* 2.9 33.1 + - - +
96D ASP* 3.6 12.5 - - - +
98D VAL* 1.3 72.0 - - - +
100D GLU* 1.3 67.2 + - - +
101D LEU 3.0 1.6 - - - -
102D LYS* 3.1 6.6 + - + +
103D GLN* 2.8 38.4 + - - +
143D VAL* 4.0 26.9 - - + +
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Residues in contact with GLU 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D TYR* 3.3 31.7 + - - +
70D LYS* 3.7 17.8 + - - +
96D ASP 2.9 12.4 + - - +
97D ILE* 3.0 10.5 + - - +
99D GLN* 1.3 76.7 - - - +
101D LEU* 1.3 60.7 + - - +
103D GLN* 3.4 9.0 + - - +
104D GLN* 3.1 42.7 + - + +
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Residues in contact with LEU 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LEU* 4.2 11.9 - - + -
66D TYR* 3.2 22.9 - - + +
75D ASN 3.4 28.7 - - - +
76D GLN* 5.0 1.1 - - - -
77D TYR* 4.1 22.2 - - + +
80D VAL* 4.3 14.6 - - + -
97D ILE* 3.0 33.5 + - + +
98D VAL* 3.5 6.7 - - - +
100D GLU* 1.3 73.8 - - - +
102D LYS* 1.3 60.1 + - - +
103D GLN 3.1 1.8 - - - -
104D GLN* 3.1 12.0 + - - +
105D ASN* 2.8 31.6 + - - +
108D LEU* 3.9 14.5 - - + +
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Residues in contact with LYS 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D VAL* 2.8 22.6 + - + +
99D GLN* 3.1 7.6 + - + +
101D LEU* 1.3 72.7 - - - +
103D GLN* 1.3 67.7 + - - +
105D ASN 3.1 22.7 - - - +
106D PRO* 3.2 13.8 + - + +
108D LEU* 2.9 40.7 + - + +
110D TYR* 4.5 4.5 - - - -
143D VAL* 3.7 34.1 - - + -
145D ASP* 2.5 38.2 + - - -
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Residues in contact with GLN 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D GLN* 2.8 24.3 + - - +
100D GLU* 3.4 12.6 - - + +
102D LYS* 1.3 86.4 - - - +
104D GLN* 1.3 67.7 + - + +
106D PRO* 3.9 10.2 - - - +
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Residues in contact with GLN 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D LYS* 3.7 8.1 + - - +
75D ASN* 3.3 41.5 + - - +
76D GLN* 4.5 11.3 - - - +
100D GLU* 3.1 33.5 - - + +
101D LEU* 3.1 11.5 + - - +
103D GLN* 1.3 78.2 - - + +
105D ASN* 1.3 60.6 + - + +
106D PRO* 3.5 6.5 - - - +
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Residues in contact with ASN 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D TYR 3.2 25.5 - - - +
78D ASP* 4.2 9.7 - - - +
101D LEU 2.8 13.4 + - - +
102D LYS* 3.1 12.2 - - - +
104D GLN* 1.3 76.1 - - + +
106D PRO* 1.3 62.9 - - - +
107D ARG* 2.6 43.6 - - - +
108D LEU* 3.1 34.4 + - + +
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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
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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) + - + + + + + -
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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