Contacts of the helix formed by residues 110 - 126 (chain 1) in PDB entry 6Q8W
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 VAL 110 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171 LEU 4.5 5.6 - - - +
201 HIS* 4.4 19.1 - - + +
211 VAL* 3.6 31.6 - - + -
261 SER* 5.1 4.7 - - - +
311 TYR* 6.1 1.1 - - + -
321 TYR* 5.9 6.5 - - + -
1061 ILE* 3.1 34.8 + - + +
1091 ASP* 1.3 84.0 - - - +
1111 PRO* 1.4 63.6 - - - +
1121 HIS 3.5 1.6 - - - -
1131 LEU* 3.6 31.8 - - + +
1141 LEU* 3.9 2.9 + - - +
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Residues in contact with PRO 111 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261 SER 5.2 0.7 - - - +
271 TRP* 4.6 15.3 - - + +
1061 ILE 4.2 3.6 - - - +
1071 LEU* 3.6 15.3 - - - +
1081 GLU 4.7 4.5 - - - +
1091 ASP 3.6 7.2 - - - +
1101 VAL* 1.4 85.6 - - - +
1121 HIS* 1.3 69.0 + - + +
1141 LEU* 2.9 25.1 + - + +
1151 ILE* 2.9 16.2 + - + +
1441 ARG* 4.2 11.2 - - + +
1451 LEU* 3.8 22.9 - - + -
1481 ALA* 3.5 26.7 - - + -
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Residues in contact with HIS 112 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271 TRP 4.5 8.9 + - - -
281 THR 4.9 2.0 - - - -
291 LEU* 4.3 31.0 - - + +
321 TYR* 3.9 17.8 + - + -
381 TYR* 3.5 34.5 + + + -
1101 VAL 3.5 0.2 - - - -
1111 PRO* 1.3 83.0 - - + +
1131 LEU* 1.3 56.5 + - - +
1151 ILE* 3.7 10.0 - - - +
1161 GLU* 2.9 30.1 + - - +
1481 ALA* 3.4 42.0 + - + +
1511 GLU* 3.8 22.6 + - + -
1521 ALA* 4.4 7.6 - - + +
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Residues in contact with LEU 113 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161 THR* 5.4 5.2 - - + +
171 LEU* 4.0 25.8 - - + +
321 TYR* 3.9 25.9 - - + +
1061 ILE* 5.0 4.3 - - + -
1101 VAL* 3.6 34.4 + - + +
1121 HIS* 1.3 77.5 - - - +
1141 LEU* 1.3 58.3 + - - +
1161 GLU* 3.2 2.1 + - - +
1171 GLY* 3.0 23.4 + - - -
2251 ALA* 3.7 28.8 - - + +
2281 VAL* 3.4 44.7 - - + +
2291 PRO* 4.9 1.3 - - + -
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Residues in contact with LEU 114 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911 CYS* 3.9 15.3 - - - -
1061 ILE* 5.0 6.5 - - + -
1071 LEU* 3.7 29.6 - - + -
1101 VAL 3.9 5.1 + - - +
1111 PRO* 2.9 11.4 + - + +
1131 LEU* 1.3 81.6 - - - +
1151 ILE* 1.3 60.0 + - + +
1171 GLY* 3.2 2.0 + - - +
1181 MET* 2.9 42.9 + - - +
1321 ILE* 4.9 5.6 - - + -
1451 LEU* 4.6 14.6 - - + -
2211 VAL* 3.6 25.1 - - + +
2241 LEU* 3.6 36.1 - - + +
2251 ALA* 4.3 7.4 - - + +
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Residues in contact with ILE 115 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381 TYR* 3.8 14.1 - - - +
1111 PRO* 2.9 16.6 + - + +
1121 HIS* 3.7 15.3 - - - +
1131 LEU 3.3 0.2 - - - -
1141 LEU* 1.3 81.1 - - + +
1161 GLU* 1.3 57.6 + - - +
1181 MET* 3.4 7.6 + - - +
1191 ILE* 2.9 34.5 + - + +
1321 ILE* 5.4 2.9 - - + -
1451 LEU* 5.5 3.8 - - + -
1481 ALA* 4.0 35.9 - - + +
1491 ILE* 4.3 10.1 - - + -
1521 ALA* 5.1 1.6 - - + -
1581 LEU* 4.0 33.2 - - + -
1691 PHE* 5.1 0.6 - - + -
1711 LEU* 3.7 24.9 - - + -
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Residues in contact with GLU 116 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321 TYR* 2.2 35.9 + - - +
381 TYR* 3.2 34.0 + - + -
401 THR* 3.4 12.5 + - - -
411 ALA* 3.1 37.9 + - + +
1121 HIS 2.9 16.0 + - - +
1131 LEU 3.5 4.7 - - - +
1151 ILE* 1.3 74.5 - - - +
1171 GLY* 1.3 64.4 + - - +
1191 ILE* 3.2 10.1 + - - +
1201 LEU* 3.0 32.4 + - + +
2281 VAL* 4.2 14.6 - - + -
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Residues in contact with GLY 117 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1131 LEU 3.0 13.0 + - - -
1141 LEU 3.2 2.9 + - - -
1161 GLU* 1.3 76.3 - - - +
1181 MET* 1.3 55.9 + - - +
1201 LEU* 3.3 5.5 + - - +
1211 ALA* 3.0 27.4 + - - +
2241 LEU* 3.2 30.1 - - - +
2271 VAL* 4.3 9.3 - - - +
2281 VAL* 3.7 8.9 - - - +
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Residues in contact with MET 118 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891 LEU* 3.5 25.7 - - + +
911 CYS* 3.7 38.8 - - + +
1141 LEU* 2.9 27.1 + - - +
1151 ILE* 3.8 4.7 - - - +
1171 GLY* 1.3 72.6 - - - +
1191 ILE* 1.3 61.0 + - - +
1211 ALA* 4.4 1.1 - - - -
1221 GLY 2.9 22.3 + - - -
1311 TYR 4.1 3.6 - - - +
1321 ILE* 3.9 19.7 - - + -
1691 PHE* 3.3 20.8 - - + -
1711 LEU* 3.6 28.3 - - + -
2241 LEU* 3.5 22.7 - - + -
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Residues in contact with ILE 119 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381 TYR* 4.2 22.9 - - + -
411 ALA* 4.2 15.0 - - + -
451 LEU* 4.1 28.7 - - + -
1151 ILE* 2.9 25.8 + - + +
1161 GLU* 3.2 9.6 + - - +
1181 MET* 1.3 77.0 - - - +
1201 LEU* 1.3 58.3 + - + +
1221 GLY* 3.4 0.7 + - - -
1231 TYR* 2.9 28.9 + - - +
1571 TYR 4.1 7.9 - - - +
1581 LEU* 3.7 31.2 - - + -
1621 LEU* 4.3 10.3 - - + -
1631 PHE* 5.6 3.8 - - + -
1671 PHE* 4.7 2.8 - - + -
1691 PHE* 4.3 15.3 - - + -
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Residues in contact with LEU 120 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401 THR* 4.6 4.7 - - + -
411 ALA* 4.0 25.4 - - + +
441 VAL* 4.1 26.0 - - + -
451 LEU* 5.8 2.5 - - + +
531 VAL* 4.3 9.9 - - + +
761 TRP* 4.8 1.6 - - - -
1161 GLU* 3.0 27.9 + - + +
1171 GLY* 3.5 7.2 - - - +
1181 MET 3.3 0.2 - - - -
1191 ILE* 1.3 77.1 - - + +
1211 ALA* 1.3 63.0 + - - +
1231 TYR* 3.4 7.6 + - + +
1241 ALA* 3.0 22.2 + - - +
2271 VAL* 3.6 32.5 - - + +
2281 VAL* 4.3 8.5 - - - -
2311 MET* 3.9 20.6 - - + -
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Residues in contact with ALA 121 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761 TRP* 3.4 37.1 - - + -
891 LEU* 3.6 24.2 - - + -
1171 GLY 3.0 14.8 + - - +
1191 ILE 3.4 0.2 - - - -
1201 LEU* 1.3 75.0 - - - +
1221 GLY* 1.3 58.8 + - - +
1241 ALA* 3.0 4.3 + - - +
1251 ILE* 2.9 34.6 + - + +
2241 LEU* 4.2 9.2 - - + -
2271 VAL* 5.6 0.2 - - + -
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Residues in contact with GLY 122 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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891 LEU* 3.9 1.7 - - - +
1181 MET 2.9 18.6 + - - -
1191 ILE 3.8 1.1 - - - -
1211 ALA* 1.3 75.4 - - - +
1231 TYR* 1.3 58.0 + - - +
1251 ILE* 4.2 0.2 - - - -
1261 ARG 2.8 26.5 + - - -
1271 ALA* 2.8 31.2 + - - -
1671 PHE* 3.1 9.5 - - - -
1691 PHE* 3.9 8.1 - - - -
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Residues in contact with TYR 123 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441 VAL* 4.1 17.9 - - + -
451 LEU* 3.5 44.9 + - + -
481 LYS 2.4 34.8 + - - -
491 THR* 3.5 19.7 - - - +
501 PRO* 3.6 26.7 - - + +
531 VAL* 4.2 11.9 - - + -
1191 ILE 2.9 17.7 + - - +
1201 LEU* 3.7 6.5 - - + +
1221 GLY* 1.3 75.9 - - - +
1241 ALA* 1.3 64.6 + - - +
1251 ILE 3.5 0.2 + - - -
1261 ARG* 3.8 4.9 + - - +
1651 THR* 6.1 1.3 - - + -
1671 PHE* 3.4 29.0 - + + -
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Residues in contact with ALA 124 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501 PRO* 3.3 7.0 - - - +
531 VAL* 3.6 23.3 - - + -
541 ILE* 3.4 12.1 - - + +
761 TRP* 3.4 36.1 - - + -
1201 LEU 3.0 11.4 + - - +
1211 ALA 3.0 8.9 + - - +
1231 TYR* 1.3 78.4 - - - +
1251 ILE* 1.3 57.9 + - - +
1261 ARG* 3.1 22.3 + - - -
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Residues in contact with ILE 125 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541 ILE* 4.7 2.0 - - + -
761 TRP* 3.9 37.2 - - + +
791 MET* 4.3 23.1 - - + +
811 LYS* 5.7 4.0 - - - +
871 HIS* 3.1 22.5 + - + +
881 TYR 4.7 2.7 - - - +
891 LEU* 3.9 22.7 - - + -
1211 ALA* 2.9 20.1 + - + +
1241 ALA* 1.3 78.2 - - - +
1261 ARG* 1.3 69.9 + - - +
1271 ALA* 3.2 18.7 + - + -
2171 THR* 3.8 28.7 - - + +
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Residues in contact with ARG 126 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501 PRO* 3.5 26.5 - - + +
511 ASP* 4.9 9.3 + - - +
811 LYS* 3.1 56.4 + - - +
821 ASP* 4.6 10.3 + - - +
851 LYS 5.4 0.5 - - - +
871 HIS* 3.9 20.8 + - + +
1221 GLY 2.8 9.6 + - - -
1231 TYR 3.8 4.8 + - - +
1241 ALA 3.1 20.5 + - - -
1251 ILE* 1.3 80.7 - - - +
1271 ALA* 1.3 59.6 - - - +
1281 THR* 3.4 14.2 + - + +
1671 PHE* 3.9 13.2 - - + -
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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
------------------------------------------------------------
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