Contacts of the helix formed by residues 127 - 142 (chain X) in PDB entry 3N5N
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 GLN 127 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126X THR* 1.3 78.4 + - - +
128X VAL* 1.3 66.6 + - - +
129X ALA* 3.2 6.5 - - + +
130X THR* 3.0 24.5 + - + +
131X VAL* 3.1 9.4 + - - +
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Residues in contact with VAL 128 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95X ARG* 3.8 29.2 - - - +
97X LEU* 3.9 29.2 - - + -
99X TRP* 4.2 8.1 - - + -
123X LEU* 3.7 25.8 - - + -
126X THR 3.8 1.2 + - - -
127X GLN* 1.3 72.2 - - - +
129X ALA* 1.3 64.6 + - - +
131X VAL* 3.1 12.4 + - - +
132X ILE* 3.1 15.5 + - + +
273X ALA* 6.4 0.4 - - + -
107Y MET* 4.1 10.8 - - + -
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Residues in contact with ALA 129 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127X GLN* 3.2 4.8 - - + +
128X VAL* 1.3 80.4 - - - +
130X THR* 1.3 66.6 + - + +
132X ILE* 3.9 16.8 - - - +
133X ASN* 4.1 9.4 + - - +
105Y ASP* 5.7 0.9 - - - +
107Y MET* 5.6 5.1 - - + +
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Residues in contact with THR 130 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126X THR* 3.0 22.8 + - - +
127X GLN* 3.0 15.5 + - + +
129X ALA* 1.3 80.7 - - + +
131X VAL* 1.3 66.8 + - - +
132X ILE 3.1 2.9 + - - -
133X ASN* 3.2 19.8 + - - +
134X TYR* 3.2 26.0 - - - -
162X GLY 4.8 3.9 + - - -
163X LEU* 4.4 8.0 - - - +
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Residues in contact with VAL 131 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99X TRP* 3.5 26.7 - - + -
119X SER* 4.9 1.1 - - - +
122X MET* 3.7 47.6 - - + +
123X LEU* 4.1 11.7 - - + -
126X THR* 3.8 15.9 - - + +
127X GLN 3.1 12.5 + - - +
128X VAL 3.1 7.7 + - - +
130X THR* 1.3 76.8 + - - +
132X ILE* 1.3 63.1 + - - +
134X TYR* 3.2 5.5 + - - +
135X TYR* 2.9 31.6 + - + +
163X LEU* 5.0 3.4 - - + -
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Residues in contact with ILE 132 (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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96X ASP 5.5 0.4 - - - +
97X LEU* 3.8 13.7 - - + -
98X PRO* 3.4 26.4 - - + +
99X TRP* 3.3 34.3 - - + -
128X VAL* 3.1 17.3 + - + +
129X ALA* 3.9 12.3 - - - +
130X THR 3.1 0.8 - - - -
131X VAL* 1.3 77.7 - - - +
133X ASN* 1.3 69.3 + - - +
135X TYR* 3.6 5.8 + - - +
136X THR* 3.7 16.2 + - - +
104Y GLU* 3.9 26.7 - - + +
105Y ASP* 5.9 1.6 - - - +
107Y MET* 4.9 9.0 - - + -
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Residues in contact with ASN 133 (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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129X ALA 4.1 11.5 + - - +
130X THR* 3.2 16.9 + - - +
132X ILE* 1.3 81.8 - - - +
134X TYR* 1.3 73.9 + - + +
136X THR* 4.1 2.8 + - - -
137X GLY* 4.0 11.6 + - - -
104Y GLU* 3.9 18.2 - - - +
105Y ASP* 4.8 5.5 - - - +
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Residues in contact with TYR 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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122X MET* 4.1 4.5 - - + -
130X THR* 3.2 25.4 - - - -
131X VAL 3.2 4.1 + - - +
133X ASN* 1.3 87.7 - - + +
135X TYR* 1.3 66.5 + - - +
137X GLY* 3.4 1.8 + - - +
138X TRP* 3.0 25.1 + - - +
158X GLN 5.8 0.4 - - - -
159X LEU* 3.7 21.0 - - - +
160X TRP 4.5 0.4 - - - -
161X ALA 2.9 28.6 + - - -
162X GLY* 3.5 17.8 + - - -
163X LEU* 3.6 37.2 - - + -
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Residues in contact with TYR 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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98X PRO* 3.9 21.3 - - + -
99X TRP* 3.6 36.7 - + + +
102X ARG* 3.6 15.4 - - - -
115X ALA* 3.0 37.2 + - - +
118X VAL* 4.0 13.0 - - + -
119X SER* 3.6 34.8 - - - -
122X MET* 3.8 12.9 - - - -
131X VAL* 2.9 18.7 + - + +
132X ILE* 4.1 2.9 - - - +
133X ASN 3.5 0.2 - - - -
134X TYR* 1.3 76.5 - - - +
136X THR* 1.3 67.5 + - - +
138X TRP* 3.2 1.7 + - - +
139X MET* 3.0 45.2 + - + +
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Residues in contact with THR 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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98X PRO* 3.9 23.7 - - - +
102X ARG* 5.3 4.1 + - - +
132X ILE* 3.7 13.5 + - - +
133X ASN 4.5 2.7 - - - -
134X TYR 3.3 0.4 - - - -
135X TYR* 1.3 82.3 - - - +
137X GLY* 1.3 57.7 + - - +
139X MET* 3.5 3.7 + - - +
140X GLN* 2.9 27.4 + - - +
91Y ASP* 5.7 0.2 - - - -
260Y ARG* 3.4 45.8 - - + +
263Y ASP* 4.4 3.8 - - - +
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Residues in contact with GLY 137 (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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133X ASN 4.0 5.6 + - - -
134X TYR* 3.4 6.4 + - - -
135X TYR 3.3 0.4 - - - -
136X THR* 1.3 75.6 - - - +
138X TRP* 1.3 67.4 + - - +
140X GLN* 3.3 9.1 + - - +
141X LYS* 3.1 21.3 + - - +
159X LEU* 4.4 12.0 - - - +
91Y ASP* 4.3 13.5 - - - -
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Residues in contact with TRP 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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114X TYR* 3.2 20.5 + - - -
118X VAL* 3.7 22.7 - - + +
122X MET* 3.7 21.5 - - + -
134X TYR 3.0 18.2 + - - +
135X TYR 3.5 4.0 - - - +
137X GLY* 1.3 74.8 - - - +
139X MET* 1.3 70.1 + - - +
141X LYS* 3.0 5.2 + - - +
142X TRP* 2.8 51.0 + + - +
148X LEU* 3.6 35.0 - - + -
156X VAL* 4.1 20.4 - - + -
159X LEU* 4.0 27.4 - - + +
160X TRP* 3.6 25.8 - + - -
169X GLY 4.8 4.0 - - - -
172X LEU* 3.9 15.9 - - + -
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Residues in contact with MET 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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102X ARG* 3.7 44.2 + - - +
111X ARG 5.2 0.7 - - - +
114X TYR* 3.5 33.4 - - + -
115X ALA* 4.0 9.4 - - + -
118X VAL* 4.4 6.5 - - - -
135X TYR* 3.0 49.5 + - + +
136X THR* 4.1 2.5 - - - +
138X TRP* 1.3 87.4 - - - +
140X GLN* 1.3 62.7 + - - +
142X TRP 4.0 2.9 - - - -
143X PRO* 3.1 39.5 - - + +
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Residues in contact with GLN 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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102X ARG* 5.3 1.1 - - - +
136X THR 2.9 19.1 + - - +
137X GLY* 3.4 9.9 - - - +
138X TRP 3.1 0.2 - - - -
139X MET* 1.3 78.6 - - - +
141X LYS* 1.3 62.7 + - + +
143X PRO* 3.9 6.6 - - - +
83Y ARG* 6.1 0.2 - - - +
84Y GLY* 4.1 19.8 + - - -
87Y LEU* 3.8 22.9 - - + +
88Y SER* 4.9 10.3 - - - +
91Y ASP* 4.2 5.4 - - - +
257Y ASP* 5.0 2.0 - - - +
260Y ARG* 3.0 44.4 + - - +
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Residues in contact with LYS 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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137X GLY 3.1 11.6 + - - +
138X TRP* 3.0 4.7 + - - +
140X GLN* 1.3 83.5 - - + +
142X TRP* 1.3 104.3 + - + +
143X PRO* 3.5 6.1 - - - +
147X ASP* 4.6 2.4 - - - +
155X GLU* 4.4 22.2 + - - +
159X LEU* 4.0 26.7 - - + -
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Residues in contact with TRP 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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114X TYR* 2.7 29.8 + - - +
138X TRP* 2.8 49.5 + + - +
139X MET* 3.5 8.5 - - - +
141X LYS* 1.3 113.0 - - + +
143X PRO* 1.3 61.3 - - - +
144X THR 3.2 2.7 - - - -
147X ASP* 3.4 25.9 + - + -
148X LEU* 3.9 19.3 - - + +
151X ALA* 3.4 29.7 - - + +
155X GLU* 3.8 33.7 + - + -
156X VAL* 3.9 5.8 - - + -
159X LEU* 3.8 28.3 - - + -
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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