Contacts of the helix formed by residues 98 - 118 (chain A) in PDB entry 1TYI
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 PHE 98 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ALA* 6.2 0.7 - - + -
55A MET* 3.9 15.9 - - + -
64A ILE* 3.4 23.3 - - + -
67A LEU* 3.7 29.8 - - + +
68A ARG* 3.2 59.7 - - + -
71A ARG* 3.5 31.4 - - - +
97A LEU* 1.4 82.5 - - + +
99A GLU* 1.4 50.9 + - - +
100A PHE 3.4 0.4 - - - -
101A CYS* 3.2 4.3 + - - +
102A GLN* 2.6 71.2 + - - +
144A VAL* 5.2 3.6 - - + +
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Residues in contact with GLU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A TYR* 4.1 10.9 + - - +
49A LYS* 4.9 16.3 - - + +
71A ARG* 2.7 40.8 + - - +
95A ASP* 3.6 3.0 + - - +
98A PHE* 1.4 73.2 - - - +
100A PHE* 1.3 87.1 + - + +
102A GLN* 3.2 11.8 + - - +
103A LEU* 2.7 33.0 + - + +
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Residues in contact with PHE 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 5.6 0.3 - - - +
12A ASN* 3.9 11.0 - - + -
13A TYR* 2.9 83.6 - + + -
15A TYR* 6.3 0.9 - - + -
94A PHE* 5.3 0.2 - - + -
95A ASP* 2.9 35.4 + - + -
96A GLY* 2.9 33.7 - - - +
98A PHE 3.4 0.2 - - - -
99A GLU* 1.3 108.3 - - + +
101A CYS* 1.3 51.3 + - - +
103A LEU* 3.2 4.3 + - - +
104A SER* 2.7 36.2 + - - -
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Residues in contact with CYS 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TYR* 4.3 7.2 - - - -
96A GLY 2.9 26.9 + - - -
97A LEU 2.9 22.0 - - - +
98A PHE 3.2 2.7 + - - +
100A PHE* 1.3 77.8 - - - +
102A GLN* 1.3 50.5 + - - +
104A SER* 3.1 10.4 + - - -
105A THR* 2.8 36.2 + - - -
130A LEU* 5.8 5.8 - - - -
141A PHE 5.6 0.2 - - - -
142A CYS* 5.8 0.2 - - - -
143A TYR* 3.3 27.6 - - - -
144A VAL* 3.4 26.5 - - + +
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Residues in contact with GLN 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LYS* 4.0 13.9 - - + +
50A ALA* 3.1 44.3 + - - +
51A ASN* 5.2 0.4 - - - +
52A ALA 5.5 0.6 - - - +
55A MET* 3.4 22.0 - - + +
68A ARG* 4.7 3.8 - - - +
71A ARG* 4.9 0.2 + - - -
98A PHE* 2.6 62.6 + - - +
99A GLU* 3.3 9.4 - - - +
101A CYS* 1.3 70.6 - - - +
103A LEU* 1.3 57.0 + - - +
105A THR* 3.6 6.1 - - - -
106A GLY 2.7 29.8 + - - -
144A VAL* 5.4 1.1 - - - -
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Residues in contact with LEU 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ASP* 5.0 0.2 - - + -
9A ASP* 4.7 3.4 - - + -
10A VAL* 3.4 20.9 - - + +
13A TYR* 2.8 36.3 - - + +
47A PRO* 3.3 48.7 - - + +
48A HIS 3.3 21.0 - - - +
49A LYS* 4.0 21.5 - - + +
99A GLU* 2.7 14.5 + - + +
100A PHE 3.3 8.7 - - - +
102A GLN* 1.3 77.4 - - - +
104A SER* 1.3 61.2 + - - +
107A GLY* 3.1 19.2 + - - -
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Residues in contact with SER 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 5.9 1.4 - - - +
100A PHE 2.7 21.4 + - - -
101A CYS* 3.2 11.4 + - - -
103A LEU* 1.3 78.0 - - - +
105A THR* 1.3 60.8 + - - +
107A GLY 3.2 1.6 + - - -
108A SER* 3.2 4.4 + - - -
125A ASN* 2.8 27.7 + - - -
127A ALA* 3.7 39.2 + - - +
128A GLY* 4.4 0.4 - - - -
130A LEU* 4.0 15.3 - - - +
146A ASP* 4.9 0.7 - - - -
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Residues in contact with THR 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ALA* 3.8 9.9 - - + -
55A MET* 5.0 4.0 - - + -
101A CYS 2.8 17.9 + - - -
102A GLN* 3.7 7.1 - - - -
103A LEU 3.3 0.2 - - - -
104A SER* 1.3 73.4 - - - +
106A GLY* 1.3 65.6 + - - +
107A GLY 3.0 1.6 - - - -
108A SER* 2.9 12.6 + - - -
109A VAL* 3.1 10.8 + - + +
144A VAL* 3.0 24.8 - - + +
145A ASN 5.6 0.2 - - - -
146A ASP* 3.9 24.0 - - - +
149A LEU* 3.3 38.1 - - + -
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Residues in contact with GLY 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A HIS* 3.2 36.4 + - - -
50A ALA* 3.7 18.2 - - - -
102A GLN 2.7 17.3 + - - -
105A THR* 1.3 73.4 - - - +
107A GLY* 1.3 50.0 + - - +
109A VAL* 3.1 5.1 + - - +
110A ALA 2.8 29.6 + - - -
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Residues in contact with GLY 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A TYR* 4.1 11.2 - - - -
47A PRO* 5.4 4.0 - - - -
48A HIS 4.0 4.6 + - - -
103A LEU 3.1 12.7 + - - -
104A SER 3.2 5.6 + - - -
105A THR 3.0 1.0 - - - -
106A GLY* 1.3 75.8 - - - +
108A SER* 1.3 52.1 + - - +
110A ALA* 3.3 8.6 + - - +
111A SER* 2.7 38.3 + - - -
125A ASN* 3.2 13.8 + - - +
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Residues in contact with SER 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A SER 3.2 2.1 + - - -
105A THR* 2.9 9.3 + - - -
107A GLY* 1.3 74.1 - - - +
109A VAL* 1.3 65.8 + - - +
111A SER* 3.0 8.5 + - - -
112A ALA* 2.9 19.3 + - - +
125A ASN* 3.0 16.9 + - - +
128A GLY* 3.9 0.3 - - - -
146A ASP* 2.8 49.8 + - - +
150A ALA* 4.4 9.4 - - - +
287A LEU* 3.6 7.3 - - - +
289A LEU* 4.3 7.6 - - - +
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Residues in contact with VAL 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A HIS* 4.6 4.0 - - - +
54A GLU* 3.0 30.1 - - + +
105A THR* 3.5 14.4 - - + +
106A GLY* 3.1 8.0 + - - +
108A SER* 1.3 73.8 - - - +
110A ALA* 1.3 67.5 + - - +
112A ALA* 2.9 7.3 + - - +
113A VAL* 2.8 34.5 + - + +
149A LEU* 3.6 19.7 - - + -
150A ALA* 5.4 2.9 - - - +
153A GLU* 2.9 42.0 - - - +
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Residues in contact with ALA 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A TYR* 3.0 36.8 + - + -
46A ARG 5.9 0.7 - - - +
47A PRO* 6.3 0.2 - - + -
48A HIS* 3.4 28.2 - - + +
106A GLY 2.8 10.4 + - - +
107A GLY* 3.6 3.4 - - - +
109A VAL* 1.3 76.7 - - - +
111A SER* 1.3 61.5 + - - +
113A VAL* 2.7 33.4 + - + +
114A LYS 3.0 4.0 + - - -
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Residues in contact with SER 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A TYR* 4.0 9.3 - - - -
107A GLY 2.7 22.0 + - - -
108A SER 3.0 6.9 + - - -
110A ALA* 1.3 76.2 - - - +
112A ALA* 1.3 61.5 + - - +
114A LYS 3.5 0.5 + - - -
115A LEU* 3.2 29.8 + - - +
123A ALA* 3.9 16.3 - - - +
125A ASN* 3.0 24.5 + - - +
287A LEU* 3.1 29.6 - - - -
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Residues in contact with ALA 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A SER 2.9 7.3 + - - +
109A VAL* 2.9 12.0 + - - +
111A SER* 1.3 76.0 - - - +
113A VAL* 1.3 66.1 + - - +
115A LEU* 3.1 4.2 + - - +
116A ASN* 3.0 30.8 + - - +
150A ALA* 5.5 5.4 - - + +
153A GLU* 4.5 10.1 - - - +
154A LEU* 4.4 22.2 - - + -
287A LEU* 3.4 20.8 - - + +
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Residues in contact with VAL 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A TYR* 4.5 2.5 - - + +
48A HIS* 6.1 0.4 - - + -
109A VAL* 2.8 37.9 + - + +
110A ALA* 2.7 31.2 + - + +
112A ALA* 1.3 70.6 - - - +
114A LYS* 1.3 58.3 + - - +
116A ASN* 3.8 3.5 - - - +
117A LYS* 2.8 63.8 + - + +
153A GLU* 4.1 7.6 - - - +
157A TYR* 6.1 0.7 - - - +
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Residues in contact with LYS 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A TYR* 2.8 32.5 - - + +
45A TYR* 3.0 35.7 + - + -
110A ALA 3.0 2.7 + - - +
111A SER 3.9 3.4 - - - +
113A VAL* 1.3 82.7 - - - +
115A LEU* 1.3 65.8 + - + +
117A LYS* 3.5 27.6 - - - +
118A GLN* 3.0 46.4 + - + +
121A ASP* 3.9 21.0 - - + +
123A ALA* 4.3 4.9 - - + -
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Residues in contact with LEU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A SER 3.2 14.3 + - - +
112A ALA* 3.1 7.4 + - - +
114A LYS* 1.3 77.1 - - - +
116A ASN* 1.3 69.1 + - - +
118A GLN 3.2 14.7 - - - +
121A ASP 3.3 14.8 - - - +
122A ILE* 3.6 5.2 - - + -
123A ALA* 2.9 35.2 - - + +
286A MET* 3.0 15.9 - - - +
287A LEU* 2.9 45.5 - - + +
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Residues in contact with ASN 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A ALA* 3.0 19.6 + - - +
113A VAL* 3.8 4.0 - - - +
115A LEU* 1.3 85.8 - - - +
117A LYS* 1.3 68.9 + - + +
118A GLN* 4.5 0.9 - - - +
154A LEU* 4.3 18.4 - - - +
157A TYR* 4.2 28.7 - - + +
247A ALA* 5.9 4.9 - - - +
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Residues in contact with LYS 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A TYR* 5.0 0.2 + - - -
113A VAL* 2.8 61.1 + - + +
114A LYS* 3.5 35.8 - - - +
116A ASN* 1.3 77.0 - - + +
118A GLN* 1.3 60.4 + - + +
119A GLN* 4.3 1.9 + - - +
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Residues in contact with GLN 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A LYS* 3.0 22.4 + - - +
45A TYR* 4.3 0.6 + - - -
114A LYS* 3.0 41.4 + - + +
115A LEU 3.2 13.0 - - - +
116A ASN 4.7 0.7 - - - -
117A LYS* 1.3 83.3 - - + +
119A GLN* 1.3 59.0 + - - +
120A THR* 3.0 12.2 + - - +
121A ASP* 2.7 58.4 + - + +
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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