Contacts of the helix formed by residues 114 - 126 (chain 2) in PDB entry 3J9X
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 ASN 114 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762 TYR* 2.9 21.2 + - + +
1122 ASN 3.7 2.5 + - - +
1132 ALA* 1.3 71.3 - - - +
1152 PRO* 1.4 62.2 - - - +
1162 GLN* 2.8 27.7 + - - +
1172 VAL* 2.7 38.4 + - + +
1182 LEU* 3.0 10.3 + - - +
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Residues in contact with PRO 115 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1042 LYS* 4.5 8.7 - - - +
1082 ILE* 3.9 29.2 - - + -
1132 ALA 3.3 9.8 - - - +
1142 ASN* 1.4 89.6 - - - +
1162 GLN* 1.3 55.3 + - - +
1182 LEU* 3.5 13.2 - - + +
1192 ASP* 2.9 38.2 + - - +
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Residues in contact with GLN 116 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662 TYR* 3.2 36.3 + - + -
1142 ASN* 2.8 22.8 + - - +
1152 PRO* 1.3 75.1 - - - +
1172 VAL* 1.3 61.9 + - + +
1192 ASP* 3.4 8.9 + - - +
1202 ALA* 3.1 18.2 + - - +
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Residues in contact with VAL 117 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622 VAL* 5.5 0.4 - - + -
632 LEU* 3.6 31.0 - - + -
662 TYR* 3.9 30.1 - - + -
682 ILE* 4.3 14.6 - - + -
762 TYR* 3.7 29.2 - - + +
1142 ASN* 2.7 22.9 + - + +
1162 GLN* 1.3 71.6 - - + +
1182 LEU* 1.3 66.4 - - - +
1202 ALA* 3.0 9.8 + - + +
1212 VAL* 2.9 21.7 + - + +
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Residues in contact with LEU 118 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762 TYR* 3.7 21.8 - - + -
792 PHE* 3.3 51.5 - - + -
1042 LYS* 4.0 17.7 - - + +
1072 TYR* 4.4 1.3 - - + -
1082 ILE* 3.3 35.4 - - + +
1132 ALA* 3.8 18.4 - - + -
1142 ASN 3.0 11.3 + - - +
1152 PRO* 3.5 13.9 - - + +
1162 GLN 3.2 0.2 - - - -
1172 VAL* 1.3 78.0 - - - +
1192 ASP* 1.3 61.4 + - - +
1212 VAL* 3.2 2.9 + - - +
1222 VAL* 3.1 21.4 + - - +
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Residues in contact with ASP 119 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1042 LYS* 2.7 36.7 + - - +
1152 PRO* 2.9 22.1 + - - +
1162 GLN* 3.6 11.9 - - - +
1182 LEU* 1.3 73.1 - - - +
1202 ALA* 1.3 60.6 + - - +
1222 VAL* 3.1 9.1 + - - +
1232 ASN* 2.8 42.3 + - - +
1292 PRO* 5.4 14.1 - - + +
1302 THR* 5.2 3.5 - - - +
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Residues in contact with ALA 120 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622 VAL* 3.8 11.2 - - + -
662 TYR* 3.5 40.8 - - + +
1162 GLN* 3.1 5.0 + - - +
1172 VAL* 3.0 10.6 + - - +
1192 ASP* 1.3 80.0 - - - +
1212 VAL* 1.3 63.1 + - - +
1232 ASN* 3.1 19.3 + - - +
1242 ILE* 3.3 18.4 + - - +
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Residues in contact with VAL 121 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592 VAL* 4.1 25.8 - - + -
622 VAL* 5.4 4.5 - - + -
632 LEU* 5.0 2.2 - - + -
762 TYR* 4.2 22.2 - - + +
792 PHE* 3.8 12.8 - - + -
802 GLY* 3.5 32.5 - - - -
1172 VAL* 2.9 21.9 + - + +
1182 LEU* 3.5 7.4 - - - +
1192 ASP 3.2 0.2 - - - -
1202 ALA* 1.3 76.6 - - + +
1222 VAL* 1.3 62.9 + - - +
1242 ILE* 3.0 19.0 + - - +
1252 ILE* 3.2 19.1 + - + +
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Residues in contact with VAL 122 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792 PHE* 3.7 23.6 - - + -
832 VAL* 4.6 7.4 - - + -
1002 ILE* 4.3 21.1 - - + -
1042 LYS* 6.0 1.8 - - + -
1182 LEU 3.1 14.2 + - - +
1192 ASP* 3.5 12.3 - - - +
1212 VAL* 1.3 76.2 - - - +
1232 ASN* 1.3 55.4 + - - +
1242 ILE 3.0 0.7 + - - -
1252 ILE* 4.6 5.2 - - - +
1262 THR* 2.5 52.1 + - + +
1282 SER 3.2 22.2 - - - +
1292 PRO* 4.3 7.2 - - + -
1302 THR* 4.4 8.1 - - + +
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Residues in contact with ASN 123 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1192 ASP* 2.8 28.4 + - - +
1202 ALA* 3.1 12.8 + - - +
1222 VAL* 1.3 75.7 - - - +
1242 ILE* 1.3 58.8 + - + +
1272 GLY* 3.2 26.0 - - - +
1282 SER* 3.1 1.0 - - - -
1292 PRO* 3.0 44.8 - - - +
123W ASN* 3.8 20.8 + - - +
124W ILE* 3.9 0.7 - - - +
127W GLY 5.1 5.6 - - - +
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Residues in contact with ILE 124 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552 VAL* 6.1 1.3 - - - -
582 ASN* 3.6 38.8 - - + +
592 VAL* 4.7 6.1 - - + +
622 VAL* 3.7 25.8 - - + -
1202 ALA 3.3 15.5 - - - +
1212 VAL* 3.4 8.1 - - - +
1222 VAL 3.0 0.8 - - - -
1232 ASN* 1.3 85.2 - - + +
1252 ILE* 1.3 71.7 + - + +
1262 THR 3.4 0.4 + - - -
1272 GLY 3.9 4.0 + - - -
58W ASN* 4.7 6.9 + - - +
123W ASN 4.4 0.2 - - - +
124W ILE* 4.1 27.6 - - + +
126W THR 5.0 0.7 - - - +
127W GLY* 3.4 34.3 - - - +
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Residues in contact with ILE 125 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552 VAL* 4.0 26.0 - - + -
592 VAL* 4.7 1.8 - - + -
802 GLY* 3.1 42.6 - - - +
832 VAL* 3.9 26.0 - - + -
842 ALA* 4.4 15.5 - - + +
872 LEU* 4.5 19.9 - - + +
1212 VAL* 3.2 19.5 + - + +
1222 VAL 4.2 1.1 - - - +
1242 ILE* 1.3 83.2 - - + +
1262 THR* 1.3 63.5 + - + +
58W ASN* 4.8 10.8 - - - +
61W ALA* 6.1 0.7 - - - +
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Residues in contact with THR 126 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832 VAL* 4.5 4.3 - - + -
872 LEU* 6.0 2.9 - - + -
962 LEU* 4.8 10.8 - - + -
1002 ILE* 4.1 21.1 - - + -
1222 VAL* 2.5 36.3 + - + +
1242 ILE 4.4 0.4 - - - -
1252 ILE* 1.3 86.2 - - + +
1272 GLY* 1.3 57.6 + - - +
1282 SER* 2.5 29.5 + - - -
61W ALA* 5.7 3.8 - - - +
62W VAL* 5.4 4.3 - - - +
65W GLN* 3.9 22.9 + - - +
124W ILE* 4.8 1.8 - - - +
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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