Contacts of the helix formed by residues 119 - 135 (chain X) in PDB entry 1SHT
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 119 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85X PHE* 3.6 11.0 - - - +
86X SER 2.9 14.8 + - - +
87X SER* 3.2 36.6 - - - +
88X GLN* 5.8 0.6 - - - -
117X GLU* 3.7 28.9 + - + +
118X THR* 1.3 77.8 - - - +
120X ILE* 1.3 63.6 + - - +
121X HIS* 3.2 24.0 - + + +
122X GLU* 3.0 25.0 + - + +
123X GLY 3.7 3.1 + - - -
155X VAL* 4.1 19.5 - - + -
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Residues in contact with ILE 120 (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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48X VAL* 4.9 2.5 - - + -
85X PHE* 3.4 35.9 - - + -
118X THR 3.3 3.6 + - - -
119X TYR* 1.3 74.2 - - - +
121X HIS* 1.3 66.6 + - - +
123X GLY* 3.0 4.2 + - - -
124X LEU* 3.0 32.7 + - + +
145X ALA* 4.5 12.3 - - + -
147X THR* 3.9 27.8 - - + +
149X GLY* 6.1 0.2 - - - -
151X LEU* 3.7 26.9 - - + -
155X VAL* 4.1 3.6 - - + -
159X ALA* 3.5 24.9 - - + -
189X ILE* 4.5 15.7 - - + -
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Residues in contact with HIS 121 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119X TYR* 3.5 37.8 - + + -
120X ILE* 1.3 80.6 - - - +
122X GLU* 1.4 83.0 + - - +
124X LEU* 3.4 7.2 + - - +
125X LYS* 2.9 29.0 + - - +
155X VAL* 3.8 24.1 - - + +
158X TYR* 3.5 59.1 - + + +
159X ALA* 3.7 8.1 - - - +
162X GLU* 3.8 7.3 - - + +
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Residues in contact with GLU 122 (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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87X SER 5.7 2.2 - - - +
88X GLN* 5.3 1.6 - - - -
89X ALA* 3.6 25.8 - - + +
119X TYR* 3.0 18.8 + - + +
121X HIS* 1.4 101.9 + - + +
123X GLY* 1.3 65.7 + - - +
125X LYS* 3.5 29.4 + - - +
126X LEU* 3.2 20.1 + - - +
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Residues in contact with GLY 123 (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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48X VAL* 3.6 22.3 - - - +
83X ILE* 3.9 13.3 - - - +
85X PHE* 4.2 6.5 - - - +
89X ALA* 3.7 14.1 - - - +
119X TYR 3.7 4.6 + - - -
120X ILE 3.0 7.5 + - - -
122X GLU* 1.3 76.8 - - - +
124X LEU* 1.3 64.5 + - - +
126X LEU* 3.3 5.5 + - - +
127X ALA 3.3 15.4 + - - -
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Residues in contact with LEU 124 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48X VAL* 3.9 10.9 - - + +
120X ILE* 3.0 28.9 + - + +
121X HIS* 3.7 2.9 - - - +
123X GLY* 1.3 74.6 - - - +
125X LYS* 1.3 57.7 + - - +
127X ALA* 3.1 8.4 + - - +
128X ASN* 2.9 32.1 + - - +
143X ILE* 3.8 31.6 - - + -
145X ALA* 4.8 9.6 - - + -
159X ALA* 3.8 29.2 - - + +
162X GLU* 3.6 21.1 - - + -
163X ALA* 4.5 5.8 - - + +
166X SER* 4.9 2.6 + - - +
173X VAL* 5.0 9.2 - - + -
189X ILE* 4.5 13.9 - - + -
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Residues in contact with LYS 125 (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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121X HIS 2.9 17.8 + - - +
122X GLU* 3.6 30.3 + - - +
123X GLY 3.2 0.4 - - - -
124X LEU* 1.3 75.4 - - - +
126X LEU* 1.3 57.3 + - + +
128X ASN* 3.2 2.8 + - + +
129X GLU* 2.9 52.5 + - + +
162X GLU* 3.7 27.9 - - - +
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Residues in contact with LEU 126 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83X ILE* 3.9 13.2 - - + -
89X ALA* 3.5 42.4 - - + +
90X THR* 3.7 15.7 - - - +
91X ILE* 4.0 21.4 - - + +
122X GLU 3.2 9.1 + - - +
123X GLY 3.8 6.3 - - - +
124X LEU 3.3 0.4 - - - -
125X LYS* 1.3 74.1 - - + +
127X ALA* 1.3 65.9 + - - +
129X GLU* 3.5 25.2 + - + +
130X GLN* 3.3 26.2 + - - +
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Residues in contact with ALA 127 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46X TYR* 4.0 21.7 - - + -
48X VAL* 4.1 10.3 - - + -
83X ILE* 3.5 19.1 - - + +
123X GLY 3.3 3.4 + - - -
124X LEU 3.1 9.5 + - - +
126X LEU* 1.3 77.1 - - - +
128X ASN* 1.3 65.0 + - - +
130X GLN* 3.1 4.2 + - - +
131X ILE* 3.0 27.0 + - - +
143X ILE* 3.9 22.0 - - + -
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Residues in contact with ASN 128 (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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124X LEU 2.9 11.1 + - - -
125X LYS* 3.2 7.6 + - + +
127X ALA* 1.3 75.0 - - - +
129X GLU* 1.3 57.0 + - + +
131X ILE* 3.2 9.9 + - - +
132X GLN* 2.9 40.4 + - - +
143X ILE* 3.7 6.9 - - - +
162X GLU* 2.7 55.1 + - - +
165X ILE* 3.8 4.1 - - + +
166X SER* 2.5 35.0 + - - +
169X LEU* 3.9 11.8 - - + +
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Residues in contact with GLU 129 (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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125X LYS* 2.9 52.6 + - + +
126X LEU* 3.5 27.0 - - + +
127X ALA 3.3 0.2 - - - -
128X ASN* 1.3 76.8 - - + +
130X GLN* 1.3 56.8 + - + +
132X GLN* 3.4 15.4 + - - +
133X LYS* 3.0 27.7 + - - +
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Residues in contact with GLN 130 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46X TYR* 3.5 24.8 + - + +
81X SER* 3.0 20.7 + - - -
83X ILE* 3.8 12.5 - - - +
91X ILE* 3.9 24.2 - - + +
94X PRO* 3.7 6.9 - - - +
95X LEU* 3.0 33.7 + - + +
126X LEU 3.3 15.4 + - - +
127X ALA 3.1 3.2 + - - +
129X GLU* 1.3 75.3 - - + +
131X ILE* 1.3 56.9 + - - +
133X LYS* 3.2 12.3 + - - +
134X ALA* 2.8 35.0 + - - +
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Residues in contact with ILE 131 (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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46X TYR* 3.4 29.6 - - + -
127X ALA 3.0 18.7 + - - +
128X ASN* 3.5 14.4 - - - +
130X GLN* 1.3 76.3 - - - +
132X GLN* 1.3 59.0 + - - +
134X ALA* 3.3 5.1 + - - +
135X GLY 3.1 6.9 + - - -
136X GLY* 2.8 32.1 + - - -
139X THR* 4.0 9.0 - - - +
141X SER* 3.9 28.3 - - - +
143X ILE* 3.9 27.8 - - + -
169X LEU* 4.1 21.1 - - + +
171X ALA* 4.0 8.1 - - + -
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Residues in contact with GLN 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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128X ASN* 2.9 30.7 + - - +
129X GLU* 3.6 14.4 + - - +
131X ILE* 1.3 77.2 - - - +
133X LYS* 1.3 62.1 + - - +
135X GLY* 3.2 14.2 + - - -
136X GLY* 3.8 7.0 + - - +
165X ILE* 5.6 2.6 - - - +
169X LEU* 3.7 28.9 - - + +
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Residues in contact with LYS 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 GLU 3.0 17.2 + - - +
130X GLN* 3.8 11.9 - - - +
132X GLN* 1.3 76.6 - - - +
134X ALA* 1.3 59.3 + - - +
135X GLY* 3.5 0.9 + - - -
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Residues in contact with ALA 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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44X ASP* 4.7 0.7 - - - +
46X TYR* 4.4 10.3 - - - +
79X ARG* 4.4 17.7 + - - +
95X LEU* 4.5 5.4 - - + -
130X GLN 2.8 16.4 + - - +
131X ILE* 3.7 5.8 - - - +
132X GLN 3.2 0.2 - - - -
133X LYS* 1.3 76.2 - - - +
135X GLY* 1.3 56.5 + - - +
138X LYS* 5.4 1.6 - - - +
139X THR* 3.4 23.8 - - + +
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Residues in contact with GLY 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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131X ILE 3.1 0.4 + - - -
132X GLN 3.2 9.4 + - - -
133X LYS 3.3 1.5 - - - -
134X ALA* 1.3 79.5 - - - +
136X GLY* 1.3 67.7 + - - +
137X LEU 3.1 4.0 + - - -
138X LYS* 3.1 38.7 + - - +
139X THR* 4.2 2.9 - - - -
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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