Contacts of the helix formed by residues 114 - 125 (chain D) in PDB entry 1UHG
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 LEU 114 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112D PRO 3.8 1.7 + - - +
113D ILE* 1.3 71.5 - - - +
115D PRO* 1.3 76.0 - - + +
116D GLU* 3.9 32.8 - - + +
117D TYR* 2.9 14.0 + - + +
118D LEU 3.0 10.4 + - - -
313D SER 3.4 25.8 - - - +
314D GLY* 3.6 18.2 - - - +
315D ILE 2.9 18.5 + - - +
316D SER* 4.5 5.6 - - - +
317D SER* 4.8 12.8 - - - +
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Residues in contact with PRO 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B PRO* 4.0 15.0 - - + +
164B DSN 4.1 13.9 - - - +
113D ILE 3.2 7.6 - - - +
114D LEU* 1.3 86.5 - - + +
116D GLU* 1.3 69.6 + - - +
118D LEU* 3.7 11.6 - - + +
119D GLN* 2.9 31.5 + - - +
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Residues in contact with GLU 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B GLN* 5.1 7.0 - - + -
163B PRO* 3.5 29.3 - - - +
164B DSN 3.9 13.7 + - - -
73D CYS 5.1 2.2 - - - +
74D GLY* 4.8 2.9 - - - -
114D LEU* 3.9 31.2 - - + +
115D PRO* 1.3 96.9 - - - +
117D TYR* 1.3 60.5 + - + +
119D GLN* 3.6 4.1 + - - +
120D CYS* 3.0 27.2 + - - +
314D GLY 5.3 1.6 - - - +
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Residues in contact with TYR 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D MET* 2.8 31.0 + - - +
43D LEU* 3.9 12.1 - - + -
44D GLY* 3.7 14.6 - - - -
105D LEU* 3.9 10.2 - - - +
113D ILE* 3.9 2.7 - - + -
114D LEU* 2.9 10.1 + - + +
116D GLU* 1.3 80.4 - - - +
118D LEU* 1.3 66.3 + - - +
120D CYS* 3.0 8.5 + - + +
121D VAL* 3.0 42.6 + - + +
129D LEU* 3.6 30.9 - - + +
314D GLY 3.4 26.5 - - - +
315D ILE* 3.5 47.4 - - + +
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Residues in contact with LEU 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D ILE* 4.3 14.8 - - + +
114D LEU 3.0 10.8 + - - +
115D PRO* 3.7 12.8 - - + +
117D TYR* 1.3 78.4 - - - +
119D GLN* 1.3 58.0 + - - +
121D VAL* 3.1 12.5 - - + +
122D LYS* 3.0 30.4 + - + +
129D LEU* 4.2 28.9 - - + +
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Residues in contact with GLN 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B ASN* 5.6 4.1 - - - +
163B PRO* 3.4 29.8 - - + -
74D GLY* 2.8 31.0 + - - -
115D PRO 2.9 16.4 + - - +
116D GLU 3.7 4.5 - - - +
118D LEU* 1.3 77.1 - - - +
120D CYS* 1.3 62.8 + - - +
122D LYS* 3.3 22.5 + - + +
123D GLU* 2.9 36.5 + - - +
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Residues in contact with CYS 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D LEU* 3.2 34.8 - - - -
73D CYS* 2.0 53.2 - - + -
74D GLY* 3.9 5.4 - - - +
116D GLU 3.0 18.9 + - - +
117D TYR* 3.2 11.2 - - + +
119D GLN* 1.3 77.7 - - - +
121D VAL* 1.3 58.5 + - + +
123D GLU* 3.3 3.3 + - - +
124D LEU* 2.9 32.6 + - - +
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Residues in contact with VAL 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D MET* 4.2 19.1 - - + -
43D LEU* 4.6 5.8 - - + -
117D TYR* 3.0 47.2 + - + +
118D LEU* 3.1 26.0 - - + +
120D CYS* 1.3 76.3 - - - +
122D LYS* 1.3 58.4 + - - +
125D TYR* 2.8 48.2 + - - +
126D ARG* 4.7 0.2 - - - -
127D GLY 5.4 0.7 - - - +
128D GLY 5.5 1.1 - - - +
129D LEU* 4.4 23.6 - - + +
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Residues in contact with LYS 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D LEU* 3.0 21.1 + - + +
119D GLN* 3.5 23.7 + - - +
120D CYS 3.2 0.2 - - - -
121D VAL* 1.3 79.7 - - - +
123D GLU* 1.3 59.9 + - + +
126D ARG* 2.8 74.8 + - - +
127D GLY 5.2 2.0 - - - +
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Residues in contact with GLU 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B ASN* 5.1 5.0 + - - -
73D CYS* 5.1 0.3 - - - -
74D GLY* 2.9 25.0 + - - +
75D THR 2.8 31.0 + - - +
76D SER* 4.0 7.3 + - - -
77D VAL 4.5 2.4 + - - +
84D ARG* 3.9 10.7 + - - -
119D GLN* 2.9 29.1 + - - +
120D CYS 3.5 8.1 - - - +
122D LYS* 1.3 82.9 - - + +
124D LEU* 1.3 68.3 + - + +
126D ARG* 4.9 4.8 + - - +
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Residues in contact with LEU 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D LEU* 4.0 8.7 - - + -
73D CYS* 3.1 29.2 - - - -
77D VAL 4.0 11.7 - - - +
79D VAL* 3.3 35.9 - - + +
80D HIS* 4.7 0.7 - - - +
84D ARG* 3.1 50.8 + - - +
88D ASN* 5.6 1.7 + - - +
120D CYS* 2.9 19.0 + - - +
123D GLU* 1.3 88.4 - - + +
125D TYR* 1.3 81.6 + - + +
126D ARG 3.9 0.9 - - - -
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Residues in contact with TYR 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D SER* 3.3 30.7 - - - -
39D ALA* 3.3 15.5 - - + +
40D MET* 3.6 46.2 - - + -
43D LEU* 3.8 22.4 - - + -
80D HIS* 2.6 32.6 + - - +
83D LEU* 4.4 2.9 - - + +
84D ARG* 4.0 15.3 - - + +
121D VAL* 2.8 20.1 + - - +
124D LEU* 1.3 93.0 - - + +
126D ARG* 1.3 67.0 + - - +
128D GLY* 2.8 17.2 + - - -
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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