Contacts of the helix formed by residues 110 - 127 (chain D) in PDB entry 1S77
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 LYS 110 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109D ILE* 1.3 75.6 - - - +
111D PRO* 1.3 78.3 - - + +
112D GLU* 4.9 0.4 - - + +
113D ALA* 3.1 14.7 - - + +
114D VAL* 3.0 16.6 + - - +
153D ARG* 5.3 7.2 - - - +
155D ARG* 5.7 11.5 - - + +
747D LEU* 3.5 36.0 - - + +
748D ASN 5.2 1.8 + - - +
749D LEU* 3.6 26.5 - - - +
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Residues in contact with PRO 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D ILE* 5.6 1.6 - - + -
85D ILE* 3.7 16.3 - - + +
86D ASN* 3.2 40.4 - - - +
89D PHE* 4.9 5.8 - - + -
106D LEU 5.7 0.7 - - - +
107D GLN* 5.9 1.3 - - - +
109D ILE 3.3 4.8 - - - +
110D LYS* 1.3 82.9 - - + +
112D GLU* 1.3 67.7 + - + +
114D VAL* 2.6 37.8 + - + +
115D ALA 3.0 3.6 + - - -
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Residues in contact with GLU 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D LEU* 3.5 17.7 - - + +
79D PRO* 3.1 14.7 - - - +
81D MET* 3.8 5.2 - - - +
82D ILE* 2.9 59.1 + - + +
85D ILE* 4.2 1.7 - - - +
86D ASN* 4.2 0.9 - - - +
110D LYS* 3.6 0.6 - - - +
111D PRO* 1.3 89.3 - - + +
113D ALA* 1.3 56.5 + - - +
115D ALA* 3.4 6.4 - - + +
116D TYR* 3.0 27.9 + - - +
747D LEU* 5.6 3.1 - - + -
755D PHE* 4.2 6.0 - - + -
757D LEU* 4.2 25.3 - - + +
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Residues in contact with ALA 113 (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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109D ILE* 5.2 3.8 - - + -
110D LYS* 3.1 47.0 + - + +
111D PRO 2.9 0.4 - - - -
112D GLU* 1.3 77.8 - - - +
114D VAL* 1.3 60.1 + - - +
116D TYR 3.7 0.2 + - - -
117D ILE* 2.9 34.3 + - + +
747D LEU* 4.5 3.2 - - + +
749D LEU* 3.4 27.8 - - + +
755D PHE* 4.1 4.9 - - - -
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Residues in contact with VAL 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D MET* 5.6 0.2 - - + -
85D ILE* 4.3 12.1 - - + -
106D LEU* 4.0 30.1 - - + +
109D ILE* 3.5 30.3 - - + +
110D LYS 3.0 15.9 + - - +
111D PRO* 2.6 19.2 + - + +
113D ALA* 1.3 69.2 - - - +
115D ALA* 1.3 52.6 + - - +
117D ILE* 2.8 10.9 + - - +
118D THR* 2.6 48.2 + - - +
145D ILE* 3.7 15.2 - - + +
216D CYS* 4.2 5.6 - - - -
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Residues in contact with ALA 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D LEU* 3.9 10.3 - - + +
81D MET* 3.2 42.8 - - + -
85D ILE* 3.7 6.3 - - + +
111D PRO 3.0 1.6 + - - -
112D GLU* 3.4 16.2 - - - +
114D VAL* 1.3 80.6 - - - +
116D TYR* 1.3 55.9 + - - +
118D THR* 3.1 8.0 - - - -
119D ILE* 2.9 35.7 + - - +
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Residues in contact with TYR 116 (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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65D ALA* 5.1 2.4 + - - +
66D ASP* 4.1 8.1 + - - -
74D ILE* 4.5 24.0 - - + -
78D LEU* 3.5 13.4 - - + +
112D GLU 3.0 8.3 + - - +
113D ALA 3.9 1.6 - - - +
115D ALA* 1.3 72.0 - - - +
117D ILE* 1.3 62.3 + - - +
118D THR 2.9 4.4 + - - -
119D ILE* 4.6 1.8 - - + +
120D LYS* 2.7 76.7 + - + +
749D LEU* 4.3 6.7 - - + -
752D LEU* 4.0 21.7 + - + -
753D GLY* 4.8 4.9 - - - -
754D GLN 4.1 9.9 + - - -
755D PHE* 3.3 69.5 - + + -
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Residues in contact with ILE 117 (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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109D ILE* 4.3 15.5 - - + -
113D ALA* 2.9 24.4 + - + +
114D VAL* 2.8 8.6 + - - +
116D TYR* 1.3 76.2 - - + +
118D THR* 1.3 58.4 + - - +
121D THR* 2.8 28.6 + - - -
141D ILE* 5.0 1.2 - - - -
144D ALA* 3.4 32.0 - - + +
145D ILE* 4.0 8.3 - - + +
148D GLU* 3.3 38.6 - - + +
749D LEU* 4.0 11.7 - - + -
752D LEU* 3.3 30.7 - - + -
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Residues in contact with THR 118 (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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81D MET* 3.9 5.9 - - + +
114D VAL* 2.6 35.4 + - - +
115D ALA* 3.1 13.8 - - - -
116D TYR 2.9 0.8 + - - -
117D ILE* 1.3 72.3 - - - +
119D ILE* 1.3 56.1 + - - +
121D THR* 2.8 8.3 + - - -
122D THR* 2.7 43.3 + - + +
141D ILE* 4.0 18.7 - - + +
145D ILE* 4.6 0.4 - - - +
216D CYS* 4.0 17.1 - - + +
220D LEU* 3.3 30.3 - - + -
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Residues in contact with ILE 119 (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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73D LEU* 6.2 0.9 - - + -
74D ILE* 4.9 20.6 - - + +
77D LEU* 4.3 8.3 - - + -
78D LEU* 3.9 35.7 - - + +
81D MET* 4.2 12.1 - - + -
115D ALA 2.9 19.0 + - - +
116D TYR* 4.1 2.2 - - + +
118D THR* 1.3 72.0 - - - +
120D LYS* 1.3 60.0 + - - +
121D THR 2.8 11.2 + - - -
122D THR* 3.0 22.1 + - - -
123D LEU* 3.2 21.0 + - + +
220D LEU* 3.9 11.2 - - + -
224D THR* 4.9 0.4 - - + -
226D MET* 3.4 39.3 - - + -
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Residues in contact with LYS 120 (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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62D GLY 5.7 0.7 - - - -
63D GLU* 5.4 9.3 - - - +
65D ALA* 3.8 25.5 - - + +
66D ASP* 3.7 22.0 + - - -
74D ILE* 5.6 0.6 - - - +
116D TYR* 2.7 53.8 + - + +
119D ILE* 1.3 72.4 - - - +
121D THR* 1.3 58.0 + - - +
123D LEU* 5.2 0.2 - - - -
124D ALA* 3.1 25.1 + - + +
752D LEU* 2.4 59.5 + - + +
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Residues in contact with THR 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D ILE 2.8 22.9 + - - -
118D THR 2.8 3.7 + - - -
120D LYS* 1.3 81.2 + - - +
122D THR* 1.3 65.8 + - - +
123D LEU 3.0 2.8 + - - -
124D ALA* 3.2 13.6 + - + +
125D CYS* 3.3 18.3 - - - -
137D VAL* 4.7 0.6 - - + +
140D ALA* 3.6 33.2 - - + +
141D ILE* 3.8 16.4 - - + +
144D ALA* 3.9 12.0 - - + +
752D LEU* 4.1 7.6 - - - +
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Residues in contact with THR 122 (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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118D THR 2.7 26.1 + - - +
119D ILE* 3.0 14.0 + - - -
121D THR* 1.3 73.3 - - - +
123D LEU* 1.3 67.8 + - - +
125D CYS* 4.1 2.6 - - - +
126D LEU* 3.1 31.1 + - - +
137D VAL* 4.1 18.3 - - + +
141D ILE* 3.6 23.3 - - + -
217D ILE* 5.2 0.4 - - + -
220D LEU* 3.5 27.8 - - + -
226D MET* 4.1 9.5 - - - +
227D VAL* 4.6 9.8 - - + +
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Residues in contact with LEU 123 (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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64D VAL* 5.1 7.0 - - + -
65D ALA* 5.2 12.1 - - + +
70D ALA* 5.2 6.1 - - + -
73D LEU* 4.4 7.9 - - + -
74D ILE* 5.5 3.1 - - + -
119D ILE* 3.2 20.5 + - + +
120D LYS 5.2 0.7 - - - -
121D THR 3.0 0.2 - - - -
122D THR* 1.3 82.9 + - - +
124D ALA* 1.3 49.5 + - - +
125D CYS 2.6 15.6 + - - -
126D LEU* 3.9 25.8 - - + +
127D THR* 2.6 42.3 + - + +
226D MET* 4.0 25.4 - - - -
246D LEU* 4.2 19.1 - - + -
254D ILE* 4.2 22.7 - - + -
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Residues in contact with ALA 124 (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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62D GLY* 3.7 27.6 - - - +
63D GLU* 4.6 4.3 - - - +
64D VAL 5.3 1.6 - - - +
65D ALA* 5.9 1.7 - - + +
120D LYS* 3.1 28.9 + - - +
121D THR* 3.2 11.4 + - + +
123D LEU* 1.3 74.8 - - - +
125D CYS* 1.3 64.6 + - - +
127D THR* 4.2 3.6 - - - -
128D SER* 3.1 19.2 - - - -
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Residues in contact with CYS 125 (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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121D THR* 3.3 20.4 - - - +
122D THR* 4.1 3.6 - - - +
123D LEU 2.6 2.0 + - - -
124D ALA* 1.3 86.6 - - - +
126D LEU* 1.3 57.6 + - - +
127D THR 2.9 8.7 + - - -
128D SER* 3.2 14.1 + - - -
129D ALA 3.3 14.9 + - - +
132D THR* 3.8 21.4 + - + +
136D ALA* 5.1 2.9 - - + -
137D VAL* 5.1 15.3 - - + -
140D ALA* 4.1 24.7 - - - -
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Residues in contact with LEU 126 (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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122D THR 3.1 23.3 + - - +
123D LEU* 3.0 19.4 + - + -
125D CYS* 1.3 74.9 - - - +
127D THR* 1.3 63.0 + - + +
129D ALA 4.3 6.5 - - - +
132D THR* 4.3 4.0 - - - +
137D VAL* 5.7 0.4 - - + -
226D MET* 5.7 0.4 - - + -
227D VAL* 4.4 19.3 - - + -
244D ILE* 3.2 44.4 - - + +
245D GLU* 3.6 13.0 - - - -
246D LEU* 3.5 36.5 - - + +
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Residues in contact with THR 127 (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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59D LEU* 2.8 34.1 + - + +
60D LYS* 5.0 0.2 - - - -
62D GLY* 4.7 1.0 - - - -
64D VAL* 2.8 40.2 - - + +
123D LEU* 2.6 30.6 + - + +
124D ALA* 4.2 3.5 - - - -
126D LEU* 1.3 89.4 - - + +
128D SER* 1.3 61.1 + - - +
129D ALA 3.8 2.2 - - - -
246D LEU* 5.3 9.2 - - + -
254D ILE* 6.0 2.2 - - + -
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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
------------------------------------------------------------
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