Contacts of the helix formed by residues 129 - 142 (chain X) in PDB entry 3TDD
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 TYR 129 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24J ILE* 4.1 27.6 - - + -
-1X MET* 4.8 21.6 - - + +
1X ASP 5.6 0.8 + - - -
127X HIS 3.7 0.2 + - - -
128X GLY* 1.3 73.9 - - - -
130X SER* 1.3 66.7 + - - +
131X GLY 3.2 3.4 - - - -
132X PHE* 2.9 37.8 + + + +
133X TYR* 3.5 23.4 - - + +
166X MET* 5.3 6.1 - - + -
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Residues in contact with SER 130 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1X ASP 3.8 2.6 + - - -
2X ILE* 3.5 32.8 - - - +
3X ILE 3.6 2.8 + - - -
4X LEU* 3.8 12.3 - - - -
126X ALA* 3.8 13.7 - - - -
127X HIS 3.3 17.5 + - - -
128X GLY 3.3 0.6 - - - -
129X TYR* 1.3 77.7 - - - +
131X GLY* 1.3 61.5 + - - +
132X PHE 3.4 0.2 + - - -
133X TYR* 3.4 2.5 + - - -
134X THR* 2.8 28.8 + - - +
162X LEU* 4.2 12.9 - - - +
166X MET* 5.7 1.9 - - - -
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Residues in contact with GLY 131 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133K PHE* 4.0 0.8 - - - -
25W LEU* 5.0 4.3 - - - -
126X ALA* 3.6 7.0 - - - +
128X GLY 4.4 4.2 + - - -
129X TYR 3.1 1.4 + - - -
130X SER* 1.3 79.3 - - - +
132X PHE* 1.3 59.5 + - - +
134X THR* 3.8 5.6 - - - -
135X PHE* 2.8 66.4 + - - +
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Residues in contact with PHE 132 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J ILE* 4.5 12.3 - - + -
129K SER 5.0 7.9 - - - -
132K THR* 2.8 49.6 + - + +
133K PHE* 3.6 35.9 - + - -
999K BFO 5.7 4.7 - - - -
22W SER 5.4 1.8 - - - -
24W SER* 4.1 18.4 - - - -
25W LEU* 3.8 30.0 - - + +
128X GLY 4.1 10.5 - - - -
129X TYR* 2.9 39.4 + + - +
131X GLY* 1.3 76.6 - - - +
133X TYR* 1.3 59.4 + - + +
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Residues in contact with TYR 133 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J ILE* 2.6 44.5 + - + +
25J SER* 4.3 1.8 - - - -
132K THR* 3.7 31.1 - - + +
135K TYR* 6.3 0.4 - - + -
136K GLY* 4.3 5.5 - - - -
129X TYR* 3.5 27.4 - - + +
130X SER 3.4 0.2 + - - -
131X GLY 3.2 0.4 - - - -
132X PHE* 1.3 77.8 - - + +
134X THR* 1.3 62.9 + - + +
135X PHE 3.9 0.2 - - - -
136X SER* 4.3 9.9 + - - -
137X LEU* 4.4 1.7 - - - +
161X GLU* 3.4 29.8 - - + +
162X LEU* 3.5 31.4 - - + -
165X ARG* 3.9 29.4 - - + -
166X MET* 3.2 31.9 - - + +
167X PRO* 4.1 1.7 - - - +
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Residues in contact with THR 134 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4X LEU* 3.8 15.3 - - + +
130X SER 2.8 24.2 + - - +
131X GLY* 3.3 2.6 + - - -
133X TYR* 1.3 81.0 - - - +
135X PHE* 1.3 70.4 + - - +
136X SER 3.2 2.7 - - - -
137X LEU* 3.0 18.5 + - - +
138X LEU* 3.0 16.8 + - - +
158X CYS* 3.6 38.6 - - + +
161X GLU* 5.4 0.2 - - + -
162X LEU* 3.7 27.6 - - + -
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Residues in contact with PHE 135 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133K PHE* 4.3 4.7 - - + -
165K ARG* 3.5 47.1 - - - +
25W LEU* 3.9 26.7 - - + -
26W GLY 4.6 0.7 - - - -
27W VAL* 5.6 5.2 - - + -
112X GLN* 4.8 3.8 - - - -
122X LEU* 5.9 1.1 - - + -
124X TYR* 4.2 10.8 - + - -
125X GLY* 4.1 20.2 - - - -
126X ALA* 3.8 25.1 - - + -
131X GLY* 2.8 43.5 + - - +
134X THR* 1.3 74.0 + - - +
136X SER* 1.3 56.7 + - - +
138X LEU* 4.0 17.0 - - + +
139X ASP* 2.8 35.9 + - - -
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Residues in contact with SER 136 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133K PHE* 2.9 45.6 + - - -
136K GLY* 3.6 15.4 - - - -
137K VAL* 3.7 9.9 + - - +
157K ARG* 5.0 2.3 + - - -
161K ALA* 3.9 22.8 - - - +
165K ARG* 5.6 0.2 - - - -
133X TYR 4.3 5.0 + - - -
134X THR 4.8 0.2 - - - +
135X PHE* 1.3 78.3 - - - +
137X LEU* 1.3 63.2 + - - +
139X ASP* 3.8 8.3 + - - +
140X HIS* 3.4 21.1 + - - +
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Residues in contact with LEU 137 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136K GLY* 3.4 30.1 - - - +
137K VAL* 4.4 2.5 - - - +
140K SER* 3.5 19.3 - - - +
133X TYR 4.4 4.5 - - - +
134X THR* 3.0 9.0 + - - +
136X SER* 1.3 83.2 + - - +
138X LEU* 1.3 65.3 + - - +
140X HIS* 3.1 3.9 + - + -
141X HIS* 3.0 36.5 + - + +
154X LEU* 4.7 2.2 - - + -
157X LEU* 3.9 32.1 - - + +
158X CYS* 4.0 18.4 - - - -
161X GLU* 3.8 29.8 - - + -
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Residues in contact with LEU 138 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4X LEU* 5.6 5.8 - - + -
5X GLY 5.4 1.3 - - - +
6X ILE* 4.1 17.9 - - + -
124X TYR* 3.3 45.1 - - + -
125X GLY 5.4 0.9 - - - +
134X THR* 3.0 23.5 + - - +
135X PHE* 4.0 15.9 - - + +
137X LEU* 1.3 70.1 - - - +
139X ASP* 1.3 67.0 - - - +
140X HIS 2.9 1.6 - - - -
142X TYR* 2.9 29.8 + - - +
154X LEU* 3.7 33.4 - - + -
155X LEU* 5.9 3.6 - - + -
158X CYS* 3.8 17.7 - - - -
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Residues in contact with ASP 139 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157K ARG* 5.0 1.1 - - - +
161K ALA* 5.2 1.3 - - + +
164K HIS* 3.5 21.5 + - - -
165K ARG* 2.9 40.0 + - - +
205K SER* 3.9 0.3 - - - -
206K PHE* 2.8 50.0 + - + +
207K ASN 4.4 1.4 + - - -
208K ASN* 5.5 1.4 + - - +
124X TYR* 2.5 29.8 + - - -
135X PHE 2.8 25.3 + - - +
136X SER* 3.9 8.1 - - - +
138X LEU* 1.3 72.6 - - - +
140X HIS* 1.3 58.9 + - - +
142X TYR* 4.9 1.4 + - - +
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Residues in contact with HIS 140 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137K VAL* 6.0 4.5 - - + -
141K ASN* 5.1 13.5 + - - -
157K ARG* 2.9 28.3 + - + +
203K GLU* 2.9 38.8 + - + -
205K SER* 3.4 22.6 - - - -
136X SER 3.4 11.8 + - - +
137X LEU* 3.1 8.5 + - + +
138X LEU 2.9 2.0 - - - -
139X ASP* 1.3 80.0 - - - +
141X HIS* 1.3 89.9 + + + +
142X TYR 4.5 0.2 - - - +
143X ARG* 2.8 21.4 + - - -
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Residues in contact with HIS 141 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140K SER* 5.0 5.6 - - - -
141K ASN* 5.3 3.7 + - - -
137X LEU* 3.0 25.8 + - + -
140X HIS* 1.3 96.2 - + + +
142X TYR* 1.3 65.0 + - - +
143X ARG* 3.0 21.4 + - - +
146X MET* 4.3 8.2 - - + +
154X LEU* 3.8 25.8 - - + -
157X LEU* 4.1 23.6 - - + +
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Residues in contact with TYR 142 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207K ASN* 3.5 25.8 + - + +
208K ASN* 5.2 3.8 - - + -
6X ILE* 3.9 25.1 - - + -
7X ARG* 2.5 46.5 + - - -
8X VAL* 4.4 2.0 - - - -
123X PRO* 3.6 22.6 - - + +
124X TYR* 3.6 27.8 - + + +
138X LEU 2.9 25.0 + - - +
139X ASP 4.7 1.6 - - - +
140X HIS 3.5 1.5 - - - +
141X HIS* 1.3 72.4 - - - +
143X ARG* 1.3 87.7 + - - +
144X PRO* 3.7 31.1 + - + +
146X MET* 4.1 5.4 - - - -
154X LEU* 3.9 8.6 - - + +
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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