Contacts of the helix formed by residues 108 - 123 (chain T) in PDB entry 3SDI
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 PRO 108 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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662 TYR* 5.1 5.8 - - - +
702 TYR* 5.5 7.2 - - + +
99T PHE* 3.5 26.7 - - + -
105T THR* 5.7 2.7 - - + +
106T PRO 3.4 5.1 - - - +
107T ILE* 1.3 88.3 - - + +
109T ILE* 1.3 61.5 + - - +
110T PRO* 4.3 6.5 - - + -
111T ALA* 3.0 15.5 + - + +
112T PHE* 2.9 25.1 + - - +
142T ASP* 3.5 22.2 - - + +
143T LYS* 6.4 2.0 - - - -
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Residues in contact with ILE 109 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73T HIS* 4.2 14.8 - - + -
74T ILE* 3.7 29.4 - - + -
108T PRO* 1.3 71.6 - - - +
110T PRO* 1.4 66.0 - - + +
112T PHE* 3.2 7.2 + - + +
113T ALA* 2.8 28.8 + - - +
138T PHE* 4.8 5.8 - - + -
139T GLY* 3.9 17.3 - - - -
140T GLY* 3.5 33.4 - - - +
141T VAL 4.2 0.4 - - - +
142T ASP* 3.3 9.5 + - + -
147T HIS* 3.7 28.5 - - + +
149T TYR* 3.8 15.0 - - + -
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Residues in contact with PRO 110 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108T PRO* 3.6 5.6 - - + -
109T ILE* 1.4 94.2 - - + +
111T ALA* 1.3 61.7 + - - +
113T ALA* 3.1 4.9 + - - +
114T ASP* 3.1 22.2 + - - +
142T ASP* 3.6 11.4 - - - +
147T HIS* 4.0 19.5 - - + +
149T TYR* 3.4 26.0 - - + +
157T TYR* 4.6 2.4 + - - -
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Residues in contact with ALA 111 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692 GLN 5.9 0.2 - - - -
702 TYR* 3.4 39.3 - - + -
99T PHE* 4.7 0.9 - - + -
107T ILE* 3.9 16.2 - - + -
108T PRO* 3.0 22.8 + - + +
110T PRO* 1.3 75.6 - - - +
112T PHE* 1.3 66.5 + - - +
114T ASP* 3.3 7.1 + - - +
115T ARG* 3.1 25.5 + - - +
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Residues in contact with PHE 112 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70T VAL* 3.6 26.7 - - + -
74T ILE* 3.8 35.0 - - + -
76T CYS* 4.3 4.7 - - - -
89T VAL* 6.2 0.4 - - - -
92T GLY* 3.4 36.8 - - - -
95T GLU* 5.4 1.1 - - + -
96T ALA* 4.8 1.1 - - + -
107T ILE* 3.7 23.2 - - + +
108T PRO 2.9 12.6 + - - +
109T ILE* 3.6 7.9 - - + +
111T ALA* 1.3 75.2 - - - +
113T ALA* 1.3 62.6 + - - +
115T ARG* 3.1 16.6 + - + +
116T LEU* 3.2 42.8 + - + +
138T PHE* 3.9 24.5 - + - -
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Residues in contact with ALA 113 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109T ILE 2.8 13.2 + - - +
110T PRO 3.1 9.2 + - - +
112T PHE* 1.3 78.1 - - - +
114T ASP* 1.3 57.1 + - - +
116T LEU* 3.3 4.9 + - - +
117T GLY 2.9 23.6 + - - -
138T PHE* 3.8 22.8 - - + -
149T TYR* 3.8 33.9 - - + -
151T LEU* 5.3 0.2 - - - +
157T TYR* 3.6 15.7 - - + -
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Residues in contact with ASP 114 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692 GLN* 5.3 1.4 - - - +
702 TYR* 6.3 1.6 - - + -
110T PRO 3.1 11.6 + - - +
111T ALA* 3.3 8.7 + - - +
113T ALA* 1.3 72.8 - - - +
115T ARG* 1.3 67.0 + - - +
117T GLY* 5.3 0.2 - - - -
118T GLN* 3.0 58.4 + - - +
157T TYR* 2.9 30.6 + - - +
86U ARG* 3.9 12.5 - - - +
90U LEU* 4.7 11.4 - - - +
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Residues in contact with ARG 115 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692 GLN* 5.1 3.6 + - - -
702 TYR* 2.8 29.9 + - - -
95T GLU* 3.4 72.7 + - + +
98T SER* 4.3 10.5 + - - -
99T PHE* 3.7 23.4 - - - +
103T TYR* 4.8 5.9 + - - -
107T ILE* 4.3 10.1 - - + +
111T ALA 3.1 18.9 + - - +
112T PHE* 3.1 11.6 + - + +
114T ASP* 1.3 79.4 - - - +
116T LEU* 1.3 62.6 + - + +
118T GLN* 3.8 4.7 - - - +
119T TYR* 3.3 20.4 + - - +
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Residues in contact with LEU 116 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76T CYS* 5.3 2.5 - - - -
88T LEU* 3.7 39.0 - - + +
89T VAL* 5.7 0.2 - - - -
91T ARG* 5.0 4.5 - - + -
92T GLY* 3.8 20.4 - - - +
95T GLU* 6.1 0.2 - - + -
112T PHE* 3.2 35.7 + - + +
113T ALA 3.8 5.2 - - - +
115T ARG* 1.3 76.4 - - + +
117T GLY* 1.3 68.1 + - - +
119T TYR* 3.1 5.5 + - + +
120T VAL* 2.8 27.4 + - - +
136T THR* 5.2 4.0 - - + -
138T PHE* 3.9 27.1 - - + -
151T LEU* 3.8 19.1 - - + -
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Residues in contact with GLY 117 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113T ALA 2.9 16.5 + - - -
114T ASP 3.4 2.2 + - - -
115T ARG 3.3 0.2 - - - -
116T LEU* 1.3 76.9 - - - +
118T GLN* 1.3 50.6 + - - +
120T VAL* 3.6 2.1 - - - +
121T GLN* 2.7 38.5 + - - +
151T LEU* 3.8 20.3 - - - +
155T GLY* 3.9 10.2 - - - -
157T TYR* 3.9 9.2 - - - -
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Residues in contact with GLN 118 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114T ASP* 3.0 51.0 + - - +
115T ARG* 3.8 6.3 - - - +
117T GLY* 1.3 74.6 - - - +
119T TYR* 1.3 57.8 + - - +
121T GLN* 3.5 10.4 + - - +
122T ALA* 3.0 27.4 + - - +
83U PRO 5.2 0.6 - - - +
86U ARG* 3.2 34.0 + - - +
87U ASN* 3.6 21.4 - - - +
90U LEU* 3.6 28.7 - - + +
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Residues in contact with TYR 119 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87T HIS* 2.6 31.8 + + - -
88T LEU* 3.8 19.1 - - + -
91T ARG* 3.5 66.6 + - + +
95T GLU* 5.1 0.7 - - - +
115T ARG 3.3 11.0 + - - +
116T LEU* 3.1 10.0 + - + +
118T GLN* 1.3 77.1 - - - +
120T VAL* 1.3 64.7 + - - +
122T ALA* 3.2 14.2 + - + +
123T HIS* 3.0 37.8 + + - -
132T PHE* 3.7 20.9 - + - -
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Residues in contact with VAL 120 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88T LEU* 3.5 31.2 - - + -
116T LEU 2.8 18.8 + - - +
117T GLY 3.6 2.7 - - - +
119T TYR* 1.3 77.2 - - - +
121T GLN* 1.3 61.7 + - - +
123T HIS* 3.0 20.1 + - - +
124T THR* 3.8 6.2 - - - +
132T PHE* 4.0 19.5 - - + -
151T LEU* 3.5 18.4 - - + -
152T GLU 3.7 6.7 - - - +
153T PRO* 3.6 16.2 - - + +
155T GLY* 3.4 27.6 - - - +
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Residues in contact with GLN 121 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117T GLY 2.7 22.1 + - - +
118T GLN* 3.8 11.5 + - - +
120T VAL* 1.3 74.1 - - - +
122T ALA* 1.3 69.7 + - - +
124T THR* 2.9 24.1 + - - +
125T LEU* 3.9 8.7 - - - +
154T SER 3.8 13.7 - - - +
155T GLY* 4.5 0.7 - - - -
83U PRO* 3.5 36.3 - - + +
84U ASP* 2.9 21.3 - - - +
87U ASN* 2.9 35.5 + - - +
130U ARG* 3.9 5.4 + - - -
132U LEU* 3.9 8.3 - - - +
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Residues in contact with ALA 122 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118T GLN 3.0 13.8 + - - +
119T TYR* 3.3 15.7 - - + +
120T VAL 3.2 0.2 - - - -
121T GLN* 1.3 82.7 - - - +
123T HIS* 1.3 63.3 + - + +
124T THR 3.0 5.8 + - - -
125T LEU* 3.1 27.2 + - + +
126T TYR* 3.5 20.0 - - + +
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Residues in contact with HIS 123 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125S GLN* 3.6 25.1 + - + -
12T ASN* 2.9 16.4 + - - -
87T HIS* 4.8 2.8 + - - -
119T TYR* 3.0 55.8 + + - -
120T VAL 3.0 10.0 + - - +
122T ALA* 1.3 78.7 - - + +
124T THR* 1.3 59.6 + - - +
125T LEU 3.5 0.9 - - - -
129T VAL* 3.9 24.5 - - + +
130T ARG 3.7 13.6 - - - +
131T PRO* 3.5 18.3 - - + +
132T PHE* 3.6 22.5 - + + -
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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
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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