Contacts of the helix formed by residues 100 - 119 (chain D) in PDB entry 1C7C
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 PRO 100 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A THR* 3.7 26.0 - - + -
41A THR* 4.8 0.4 - - + -
98D VAL 3.2 5.1 - - - +
99D ASP* 1.3 89.3 - - - +
101D GLU* 1.3 63.6 + - - +
102D ASN 3.0 0.7 - - - -
103D PHE* 3.0 34.7 + - + +
104D ARG* 3.7 12.4 + - - +
142D ALA* 3.7 25.1 - - + -
145D TYR* 3.5 35.0 - - + -
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Residues in contact with GLU 101 (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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94A ASP* 3.3 30.5 - - + +
96A VAL* 3.7 29.5 - - + +
99D ASP* 3.1 23.8 + - - +
100D PRO* 1.3 76.8 - - - +
102D ASN* 1.3 61.1 + - - +
104D ARG* 3.1 39.0 + - - +
105D LEU* 3.1 26.3 + - + +
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Residues in contact with ASN 102 (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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42A TYR* 4.9 1.8 + - - -
94A ASP* 5.0 5.7 - - - +
31D LEU* 4.9 1.2 - - - +
37D TRP* 5.1 2.6 - - - -
38D THR* 3.3 28.2 - - + +
41D PHE* 3.5 31.2 - - - -
98D VAL* 4.0 5.3 - - + +
99D ASP* 2.9 38.5 + - - +
101D GLU* 1.3 78.0 - - - +
103D PHE* 1.3 56.5 + - - +
105D LEU* 3.7 10.7 - - - +
106D LEU* 2.9 23.6 + - - +
147D HEM 3.4 30.0 - - + +
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Residues in contact with PHE 103 (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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92D HIS* 3.9 26.9 - + + -
98D VAL* 4.1 11.0 - - + -
100D PRO* 3.0 35.3 + - + +
102D ASN* 1.3 76.5 - - - +
104D ARG* 1.3 57.2 + - - +
106D LEU* 3.5 5.5 + - - +
107D GLY* 3.1 21.7 + - - -
134D VAL 5.3 0.7 - - - +
138D ALA* 3.7 30.6 - - + +
141D LEU* 3.6 47.1 - - + -
145D TYR* 3.6 19.5 - + - -
147D HEM 3.6 41.4 - + + +
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Residues in contact with ARG 104 (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* 4.0 7.8 + - - +
101D GLU* 3.1 45.0 + - - +
103D PHE* 1.3 75.9 - - - +
105D LEU* 1.3 65.2 + - - +
107D GLY* 3.2 2.9 + - - -
108D LYS* 3.1 28.0 + - + +
135D ALA* 6.5 0.2 - - - -
138D ALA* 4.1 23.4 + - + +
139D ASN* 3.5 24.6 + - - -
142D ALA* 5.2 6.3 - - - +
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Residues in contact with LEU 105 (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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94A ASP* 3.7 22.0 - - - +
31D LEU* 3.8 13.2 - - + -
35D TYR* 4.2 30.8 - - + -
37D TRP* 4.0 15.7 - - + +
38D THR* 4.1 17.9 - - + -
101D GLU* 3.1 29.0 + - - +
102D ASN* 3.7 12.1 - - - +
104D ARG* 1.3 77.7 - - - +
106D LEU* 1.3 62.6 + - - +
108D LYS* 3.3 19.8 + - + +
109D VAL* 3.2 25.3 + - - +
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Residues in contact with LEU 106 (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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27D ALA* 4.2 34.3 - - + +
28D LEU* 4.5 8.7 - - + +
31D LEU* 3.9 19.0 - - + +
67D VAL* 3.9 15.5 - - + -
68D LEU* 6.0 4.9 - - + -
102D ASN 2.9 17.5 + - - +
103D PHE 3.8 4.9 - - - +
105D LEU* 1.3 76.9 - - - +
107D GLY* 1.3 56.8 + - - +
109D VAL* 3.3 2.4 + - + +
110D LEU* 2.8 32.3 + - + +
147D HEM 3.3 53.2 - - + -
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Residues in contact with GLY 107 (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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103D PHE 3.1 15.3 + - - -
104D ARG* 3.2 5.6 + - - -
105D LEU 3.2 0.4 - - - -
106D LEU* 1.3 76.9 - - - +
108D LYS* 1.3 60.0 + - - +
110D LEU* 3.3 6.3 + - - +
111D VAL* 3.1 29.4 + - - +
131D GLN* 6.0 0.2 - - - -
134D VAL* 4.0 29.6 - - - +
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Residues in contact with LYS 108 (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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241A LYS* 5.6 6.5 + - - +
245A HIS* 3.6 42.3 - - + +
268A ASP* 4.9 5.3 + - - -
35D TYR* 3.4 29.6 + - - +
104D ARG* 3.1 17.6 + - + +
105D LEU* 3.3 21.8 + - + +
107D GLY* 1.3 75.9 - - - +
109D VAL* 1.3 64.9 + - + +
111D VAL* 3.3 2.1 + - - -
112D CYS* 3.2 27.7 + - - -
131D GLN* 5.9 4.0 - - - +
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Residues in contact with VAL 109 (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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264A HIS* 4.7 11.4 - - + +
27D ALA* 3.4 32.1 - - - +
30D ARG* 3.6 23.1 - - + -
31D LEU* 3.9 16.2 - - + +
34D VAL* 5.2 0.7 - - + -
35D TYR* 3.8 24.2 - - + -
105D LEU 3.2 13.4 + - - +
106D LEU* 3.7 8.5 - - + +
108D LYS* 1.3 74.0 - - + +
110D LEU* 1.3 67.9 + - - +
112D CYS* 3.1 9.5 + - - +
113D VAL* 2.9 23.8 + - + +
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Residues in contact with LEU 110 (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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15D TRP* 4.9 3.4 - - + -
23D VAL* 3.9 27.6 - - + -
27D ALA* 4.4 12.7 - - + +
68D LEU* 4.1 23.3 - - + -
71D PHE* 3.9 37.5 - - + -
106D LEU* 2.8 22.3 + - + +
107D GLY* 3.6 6.3 - - - +
109D VAL* 1.3 79.1 - - - +
111D VAL* 1.3 58.1 + - - +
113D VAL* 3.2 5.1 + - + +
114D LEU* 2.9 51.0 + - + +
130D TYR* 5.9 0.2 - - + -
134D VAL* 4.4 10.3 - - + -
147D HEM 6.5 0.7 - - + -
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Residues in contact with VAL 111 (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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245A HIS* 4.0 1.8 - - + +
249A VAL* 3.8 18.8 - - + -
107D GLY 3.1 16.1 + - - +
108D LYS* 3.7 7.2 - - - +
109D VAL 3.2 0.2 - - - -
110D LEU* 1.3 75.2 - - + +
112D CYS* 1.3 64.7 + - - +
114D LEU* 3.3 10.3 + - + +
115D ALA* 3.0 22.3 + - - +
122D PHE* 3.9 18.9 - - + -
127D GLN* 4.1 5.2 - - + -
130D TYR* 4.8 12.1 - - + -
131D GLN* 3.6 37.0 - - - +
134D VAL* 4.4 16.2 - - + -
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Residues in contact with CYS 112 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245A HIS* 4.3 7.4 - - - -
248A LEU* 4.3 20.4 - - - -
249A VAL* 4.0 20.9 - - - -
252A ALA* 3.7 5.6 - - + +
259A PHE* 4.5 9.8 - - + -
264A HIS* 3.9 31.0 - - + -
108D LYS* 3.2 18.0 + - - +
109D VAL* 3.1 9.7 + - - +
111D VAL* 1.3 76.8 - - - +
113D VAL* 1.3 57.1 + - - +
115D ALA* 3.3 7.8 + - - +
116D HIS* 2.9 28.6 + - - +
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Residues in contact with VAL 113 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23D VAL* 3.9 31.9 - - + +
26D GLU* 3.9 24.9 - - + -
27D ALA* 4.1 14.8 - - - -
30D ARG* 3.8 29.4 - - - +
109D VAL* 2.9 17.3 + - + +
110D LEU* 3.6 9.6 - - + +
112D CYS* 1.3 73.0 - - - +
114D LEU* 1.3 68.4 + - - +
116D HIS* 3.2 7.3 + - + +
117D HIS* 2.9 26.4 + - + +
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Residues in contact with LEU 114 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14D LEU* 4.7 2.2 - - + -
15D TRP* 4.5 5.4 - - + -
18D VAL* 4.3 15.3 - - + -
23D VAL* 4.4 21.5 - - + -
110D LEU* 2.9 37.8 + - + +
111D VAL* 3.3 4.2 + - + +
113D VAL* 1.3 75.3 - - - +
115D ALA* 1.3 63.3 + - - +
117D HIS* 4.6 0.7 - - + -
118D PHE* 2.9 52.2 + - + +
122D PHE* 3.8 26.4 - - + +
130D TYR* 3.8 35.9 - - + -
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Residues in contact with ALA 115 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A VAL* 3.7 29.8 - - + +
252A ALA* 4.1 3.1 - - + -
253A ALA* 3.4 18.0 - - + +
111D VAL 3.0 17.2 + - - +
112D CYS 3.6 4.9 - - - +
114D LEU* 1.3 78.5 - - - +
116D HIS* 1.3 57.4 + - - +
119D GLY* 2.9 23.7 + - - -
122D PHE* 3.6 27.5 - - + -
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Residues in contact with HIS 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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252A ALA* 3.5 20.6 - - + +
256A PRO* 2.6 49.7 + - + +
259A PHE* 3.7 26.5 + + + -
260A THR* 5.6 0.2 - - - -
26D GLU* 4.9 4.7 + - - +
30D ARG* 3.5 27.7 + - - +
112D CYS 2.9 16.8 + - - +
113D VAL* 3.2 8.4 + - - +
115D ALA* 1.3 77.4 - - - +
117D HIS* 1.3 63.3 + - - +
119D GLY* 4.1 3.5 + - - -
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Residues in contact with HIS 117 (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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17D LYS 4.9 5.5 + - - -
18D VAL* 5.9 0.6 - - - -
19D ASN 6.0 1.2 + - - -
22D GLU* 3.6 27.7 + - - -
23D VAL* 5.1 13.7 - - + +
113D VAL* 2.9 21.0 + - + +
114D LEU* 4.0 3.4 - - + +
116D HIS* 1.3 81.9 + - - +
118D PHE* 1.3 99.6 + + + +
119D GLY 3.9 0.3 + - - -
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Residues in contact with PHE 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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14D LEU* 3.7 35.9 - - + -
17D LYS* 3.7 37.7 - - + -
18D VAL* 3.9 29.2 - - + -
23D VAL* 5.8 0.2 - - + -
114D LEU* 2.9 32.6 + - + +
117D HIS* 1.3 109.3 - + + +
119D GLY* 1.3 65.8 + - - +
120D LYS* 3.3 2.3 + - - +
121D GLU* 3.3 29.8 + - + +
122D PHE* 4.4 13.0 - - + +
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Residues in contact with GLY 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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253A ALA* 3.5 29.8 - - - +
115D ALA 2.9 18.0 + - - -
116D HIS 4.1 3.5 + - - -
117D HIS 3.5 2.2 + - - -
118D PHE* 1.3 75.6 - - - +
120D LYS* 1.3 64.1 + - - -
122D PHE* 3.0 22.0 + - - +
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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