Contacts of the helix formed by residues 155 - 166 (chain I) in PDB entry 1TB6
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 ASN 155 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1C NAG 1.5 70.9 + - - +
154I PHE* 1.3 68.5 - - - +
156I GLU* 1.3 63.9 + - - +
157I THR* 2.6 32.9 + - - -
158I TYR* 3.1 6.2 + - + +
159I GLN* 3.0 22.7 + - - +
353I GLY 3.2 19.0 + - - +
354I ILE 2.7 12.5 + - - +
355I VAL 3.8 7.4 - - - +
356I ALA* 3.5 10.5 - - - +
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Residues in contact with GLU 156 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153I THR* 5.9 1.0 - - - +
154I PHE 3.2 20.6 + - - +
155I ASN* 1.3 73.5 + - - +
157I THR* 1.3 59.0 + - - +
159I GLN* 3.2 20.0 + - + +
160I ASP* 3.0 38.8 + - - +
169I LYS* 4.6 9.7 + - - +
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Residues in contact with THR 157 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C NAG 3.3 31.4 - - - -
2C NAG 3.7 21.8 - - + +
155I ASN* 2.6 17.1 + - - -
156I GLU* 1.3 71.9 - - - +
158I TYR* 1.3 62.2 - - - -
160I ASP* 3.4 10.6 + - + +
161I ILE* 3.1 31.8 + - + +
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Residues in contact with TYR 158 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C NAG 3.8 10.5 + - - +
89I MET* 2.7 31.9 + - + +
92I LEU* 3.4 36.2 - - + +
93I GLY* 4.3 3.4 - - - -
146I LEU* 3.9 17.0 - - + +
154I PHE* 6.2 0.7 - - + -
155I ASN* 3.1 16.7 + - + +
157I THR* 1.3 76.8 - - - +
159I GLN* 1.3 73.5 + - - +
161I ILE* 3.4 4.9 + - - +
162I SER* 2.8 37.9 + - - -
170I LEU* 4.8 11.2 - - + -
353I GLY 3.6 27.6 - - - +
354I ILE* 3.7 34.1 - - + +
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Residues in contact with GLN 159 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154I PHE* 4.4 19.3 - - + +
155I ASN 3.0 20.5 + - - +
156I GLU* 3.4 26.8 + - - +
158I TYR* 1.3 86.4 - - + +
160I ASP* 1.3 58.5 + - - +
162I SER* 3.1 2.8 + - - -
163I GLU* 2.9 27.7 + - - +
169I LYS* 3.4 33.6 - - + +
170I LEU* 3.0 53.1 + - - +
172I PRO* 5.1 3.2 - - - +
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Residues in contact with ASP 160 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156I GLU* 3.0 25.5 + - - +
157I THR* 3.4 10.1 + - + +
159I GLN* 1.3 76.1 - - - +
161I ILE* 1.3 63.6 + - + +
163I GLU* 3.7 4.8 + - - +
164I LEU* 3.3 23.2 + - - +
169I LYS* 4.6 12.2 + - - +
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Residues in contact with ILE 161 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C NAG 3.8 25.1 - - - +
2C NAG 3.8 7.6 - - + -
16I PRO 4.9 2.0 - - - +
17I MET* 3.7 49.6 - - + +
18I ASN 4.6 0.4 - - - +
92I LEU* 4.1 15.9 - - + -
120I HIS* 3.9 19.5 - - - +
157I THR* 3.1 20.0 + - + +
158I TYR* 3.8 4.7 - - - +
160I ASP* 1.3 75.5 - - + +
162I SER* 1.3 62.3 + - - +
164I LEU* 3.2 6.8 + - + +
165I VAL* 2.9 37.6 + - + +
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Residues in contact with SER 162 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89I MET* 4.8 6.2 - - - +
92I LEU* 5.0 1.5 - - - +
158I TYR* 2.8 36.1 + - - -
159I GLN* 3.4 6.1 - - - -
161I ILE* 1.3 77.6 - - - +
163I GLU* 1.3 56.9 + - - +
165I VAL* 4.2 5.8 - - - -
166I TYR* 2.7 45.0 + - - +
168I ALA 2.6 25.7 + - - +
169I LYS* 3.3 9.8 - - - -
170I LEU 3.9 2.9 + - - -
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Residues in contact with GLU 163 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159I GLN 2.9 16.2 + - - +
160I ASP* 4.1 5.4 - - - +
162I SER* 1.3 76.2 + - - +
164I LEU* 1.3 62.5 + - - +
167I GLY* 3.5 27.0 + - - +
168I ALA* 3.8 13.4 + - - -
169I LYS* 3.5 34.7 + - + +
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Residues in contact with LEU 164 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5I VAL* 4.0 28.5 - - + +
7I ILE* 3.4 47.2 - - + +
15I ILE* 3.9 31.4 - - + -
17I MET* 4.6 14.1 - - + -
160I ASP 3.3 17.2 + - - +
161I ILE* 3.2 6.2 + - + +
162I SER 3.2 0.4 - - - -
163I GLU* 1.3 81.8 - - - +
165I VAL* 1.3 60.3 + - - +
167I GLY* 5.3 0.2 - - - -
866I MPD 3.7 10.4 - - - +
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Residues in contact with VAL 165 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7I ILE* 4.9 2.9 - - + -
17I MET* 5.1 5.8 - - - -
85I THR* 6.0 0.5 - - - +
89I MET* 3.8 27.8 - - + +
120I HIS* 2.8 37.5 - - + +
121I PHE* 3.6 10.5 - - + -
124I ALA* 3.3 21.1 + - + +
161I ILE* 2.9 39.1 + - + +
162I SER 4.1 0.2 - - - +
164I LEU* 1.3 80.4 - - + +
166I TYR* 1.3 60.6 + - - +
167I GLY 3.6 0.4 - - - -
866I MPD 3.4 19.2 + - - +
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Residues in contact with TYR 166 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82I SER 4.9 0.5 + - - -
85I THR* 3.5 31.2 - - + -
86I ALA* 3.5 27.3 + - - +
89I MET* 3.6 34.3 - - + -
144I ASN* 3.1 47.9 + - + +
145I ARG* 4.1 10.8 + - - -
146I LEU* 3.9 25.4 - - + +
162I SER* 2.7 23.7 + - - +
165I VAL* 1.3 74.8 - - - +
167I GLY* 1.3 55.3 + - - +
168I ALA* 3.2 17.8 + - + +
216I VAL 4.6 0.5 + - - -
217I ASN* 4.2 2.9 - - - +
866I MPD 3.7 12.7 - - + +
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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