Contacts of the helix formed by residues 123 - 142 (chain D) in PDB entry 1HGC
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 THR 123 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C ARG* 3.6 2.2 - - - +
120D LYS 3.6 18.8 - - - +
121D GLU* 3.1 10.0 + - - +
122D PHE* 1.3 76.6 - - - +
124D PRO* 1.3 67.7 - - + +
125D PRO* 3.5 10.2 - - - +
126D VAL* 2.7 32.7 + - - +
127D GLN* 2.6 33.4 + - - +
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Residues in contact with PRO 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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27C GLU* 4.7 10.3 - - + -
30C GLU* 4.4 21.1 - - - +
31C ARG* 3.7 43.1 - - + +
34C LEU* 3.6 23.2 - - + +
35C SER* 4.4 3.3 + - - -
123D THR* 1.3 85.6 - - + +
125D PRO* 1.3 67.3 - - + +
127D GLN* 3.5 4.9 - - - +
128D ALA* 3.1 24.9 + - - +
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Residues in contact with PRO 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C GLU* 6.1 0.2 - - - +
34C LEU* 4.2 13.2 - - + -
7D GLU* 5.1 2.8 - - - +
123D THR* 3.1 15.3 - - - +
124D PRO* 1.3 102.8 - - + +
126D VAL* 1.3 62.6 + - + +
127D GLN 3.3 0.2 - - - -
128D ALA* 3.5 9.3 - - + +
129D ALA* 3.4 19.8 + - - +
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Residues in contact with VAL 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D ALA* 4.4 29.2 - - + +
14D LEU* 4.6 7.9 - - + -
121D GLU 4.2 11.9 - - - +
122D PHE* 3.6 26.0 - - + -
123D THR* 2.7 32.2 + - - +
125D PRO* 1.3 71.6 - - + +
127D GLN* 1.3 69.4 + - - +
129D ALA* 3.3 6.3 + - - +
130D TYR* 3.2 34.0 + - + -
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Residues in contact with GLN 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ARG* 3.0 43.8 + - - +
35C SER* 3.4 16.4 + - - +
103C HIS* 3.9 10.9 - - - -
104C CYS* 4.0 15.0 - - - -
107C VAL* 3.7 13.8 - - - +
111D VAL* 4.0 2.5 - - + -
122D PHE* 3.5 28.9 - - + -
123D THR 2.6 10.9 + - - -
124D PRO 3.5 6.7 - - - +
126D VAL* 1.3 72.9 - - - +
128D ALA* 1.3 52.5 + - - +
130D TYR* 2.9 6.8 + - - +
131D GLN* 2.8 57.3 + - + +
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Residues in contact with ALA 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LEU* 3.7 31.2 - - + +
35C SER* 3.8 13.6 - - - +
7D GLU* 4.9 5.6 - - - +
124D PRO 3.1 12.2 + - - +
125D PRO* 3.5 14.1 - - + +
126D VAL 3.2 0.2 - - - -
127D GLN* 1.3 78.8 - - - +
129D ALA* 1.3 59.9 + - - +
131D GLN* 3.6 3.8 + - - +
132D LYS* 3.4 28.4 + - + +
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Residues in contact with ALA 129 (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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3D LEU* 4.2 2.6 - - + +
7D GLU* 3.9 37.2 + - + +
10D ALA* 5.7 2.0 - - + -
11D VAL* 3.7 22.2 - - + -
125D PRO 3.4 8.3 + - - +
126D VAL* 3.3 9.3 + - - +
127D GLN 3.3 1.0 - - - -
128D ALA* 1.3 74.8 - - - +
130D TYR* 1.3 61.2 + - - +
132D LYS* 3.0 23.4 + - - +
133D VAL* 3.0 16.1 + - - +
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Residues in contact with TYR 130 (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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10D ALA 4.4 0.7 - - - -
11D VAL* 2.6 53.0 + - + +
14D LEU* 3.7 21.7 - - + +
15D TRP* 3.3 38.8 + + - +
71D PHE* 4.9 7.2 - + - -
75D LEU* 5.1 1.1 - - + -
111D VAL* 4.4 7.9 - - + -
114D LEU* 4.1 13.2 - - + -
122D PHE* 3.8 23.1 - + + -
126D VAL* 3.2 22.2 + - + +
127D GLN 2.9 8.4 + - - +
129D ALA* 1.3 79.1 - - - +
131D GLN* 1.3 60.1 + - - +
133D VAL* 2.9 15.4 + - + +
134D VAL* 2.9 39.8 + - + +
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Residues in contact with GLN 131 (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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35C SER* 3.9 22.2 - - - +
36C PHE* 3.9 17.2 - - + -
103C HIS* 2.7 31.2 + - - -
108D ASN* 3.5 20.4 + - - -
111D VAL* 3.4 10.7 - - - +
127D GLN* 2.8 36.2 + - + +
128D ALA* 3.7 9.2 - - - +
129D ALA 3.2 0.2 - - - -
130D TYR* 1.3 76.4 - - - +
132D LYS* 1.3 62.8 + - + +
134D VAL* 3.6 14.9 - - - +
135D ALA* 3.2 25.3 + - - +
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Residues in contact with LYS 132 (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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35C SER 6.0 2.0 - - - +
1D VAL* 3.8 13.0 - - + +
2D HIS 2.9 27.5 + - - +
3D LEU* 3.8 12.3 - - + -
7D GLU* 2.5 38.7 + - - +
128D ALA* 3.4 17.4 + - + +
129D ALA* 3.0 12.6 + - - +
131D GLN* 1.3 78.2 - - + +
133D VAL* 1.3 58.1 + - - +
135D ALA* 3.7 5.2 + - - +
136D GLY 3.2 19.9 + - - -
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Residues in contact with VAL 133 (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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1D VAL* 5.1 3.8 - - - -
3D LEU* 4.0 17.5 - - + -
11D VAL* 4.0 25.6 - - + -
71D PHE* 3.5 28.5 - - + -
75D LEU* 3.6 16.4 - - + -
78D LEU* 4.4 13.7 - - + -
81D LEU* 4.8 1.9 - - - +
129D ALA 3.0 15.5 + - - +
130D TYR* 2.9 15.1 + - + +
132D LYS* 1.3 74.7 - - - +
134D VAL* 1.3 59.7 + - + +
135D ALA 3.0 4.3 - - - -
136D GLY* 3.0 4.3 + - - -
137D VAL* 2.9 31.4 + - + +
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Residues in contact with VAL 134 (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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71D PHE* 4.0 22.4 - - + -
103D PHE 4.9 0.9 - - - +
104D ARG* 5.7 0.9 - - - -
107D GLY* 3.6 41.3 - - - +
108D ASN* 4.7 1.3 - - - +
110D LEU* 4.1 12.1 - - + -
111D VAL* 4.1 8.5 - - + -
114D LEU* 6.2 0.2 - - + -
130D TYR* 2.9 24.1 + - + +
131D GLN* 3.6 22.4 - - - +
133D VAL* 1.3 72.7 - - + +
135D ALA* 1.3 58.8 + - + +
137D VAL* 3.9 9.4 - - - +
138D ALA* 3.3 25.1 + - - +
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Residues in contact with ALA 135 (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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104D ARG* 6.3 1.3 - - - -
131D GLN 3.2 19.7 + - - +
132D LYS* 3.9 5.8 - - - +
133D VAL 3.0 1.0 - - - -
134D VAL* 1.3 77.2 - - + +
136D GLY* 1.3 65.0 + - - +
137D VAL 3.3 0.2 - - - -
138D ALA* 3.5 4.9 + - - +
139D ASN* 3.2 34.8 + - - +
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Residues in contact with GLY 136 (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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1D VAL* 3.5 27.6 - - - -
81D LEU* 4.2 7.4 - - - +
132D LYS 3.2 8.1 + - - -
133D VAL 3.0 4.2 + - - -
135D ALA* 1.3 78.5 - - - +
137D VAL* 1.3 55.7 + - - +
139D ASN* 3.3 8.9 + - - +
140D ALA* 2.9 30.8 + - - +
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Residues in contact with VAL 137 (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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71D PHE* 3.6 40.6 - - + +
74D GLY* 6.2 0.7 - - - -
75D LEU* 5.8 2.2 - - + -
78D LEU* 6.3 0.2 - - + -
81D LEU* 4.4 10.3 - - + +
85D PHE* 4.5 25.3 - - + -
133D VAL* 2.9 22.0 + - + +
134D VAL 4.0 4.7 - - - +
135D ALA 3.3 0.2 - - - -
136D GLY* 1.3 73.4 - - - +
138D ALA* 1.3 56.8 + - - +
140D ALA* 3.2 5.3 + - - +
141D LEU* 2.8 55.0 + - + +
147D HEM 4.3 11.7 - - + -
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Residues in contact with ALA 138 (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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100D PRO 4.9 0.7 - - - +
103D PHE* 3.9 34.6 - - + +
104D ARG* 4.1 26.2 + - + +
134D VAL 3.3 16.9 + - - +
135D ALA* 3.8 6.7 - - - +
136D GLY 3.3 0.2 - - - -
137D VAL* 1.3 79.0 - - - +
139D ASN* 1.3 62.2 + - - +
141D LEU* 4.6 0.9 - - - -
142D ALA* 3.1 28.2 + - - +
147D HEM 5.8 0.2 - - - -
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Residues in contact with ASN 139 (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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82D LYS* 4.2 12.0 + - - +
104D ARG* 5.3 8.7 + - - +
135D ALA* 3.2 23.9 + - - +
136D GLY* 3.6 7.1 - - - +
137D VAL 3.1 0.4 - - - -
138D ALA* 1.3 82.1 - - - +
140D ALA* 1.3 59.9 + - - +
141D LEU 3.2 0.2 - - - -
142D ALA* 3.8 5.5 - - - +
143D HIS* 3.1 25.5 + - - +
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Residues in contact with ALA 140 (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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81D LEU* 3.5 40.6 - - + +
82D LYS* 3.7 13.9 - - + +
85D PHE* 3.9 12.9 - - + +
89D SER* 3.8 5.7 + - - -
136D GLY 2.9 17.3 + - - +
137D VAL 3.8 3.4 - - - +
139D ASN* 1.3 76.3 - - - +
141D LEU* 1.3 58.2 + - - +
143D HIS* 2.6 29.5 + - - +
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Residues in contact with LEU 141 (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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85D PHE* 4.4 15.5 - - + -
88D LEU* 4.0 38.6 - - + +
89D SER* 2.7 24.5 + - - +
92D HIS* 4.3 11.4 - - + +
103D PHE* 3.8 21.6 - - + -
137D VAL* 2.8 20.1 + - + +
138D ALA 4.0 0.2 - - - +
140D ALA* 1.3 80.4 - - - +
142D ALA* 1.3 54.5 + - - +
143D HIS 3.2 0.4 - - - -
145D TYR* 3.3 13.3 - - - -
147D HEM 3.0 54.7 - - + -
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Residues in contact with ALA 142 (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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38A THR* 5.7 1.6 - - + +
100D PRO* 3.6 24.2 - - + -
104D ARG* 4.5 8.1 - - - +
138D ALA 3.1 21.1 + - - +
139D ASN* 3.8 7.0 - - - +
140D ALA 3.2 0.4 - - - -
141D LEU* 1.3 76.5 - - - +
143D HIS* 1.3 64.8 + - - +
144D LYS 3.4 1.1 - - - -
145D TYR* 3.3 30.2 + - - +
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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
------------------------------------------------------------
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