Contacts of the helix formed by residues 121 - 131 (chain 1) in PDB entry 3KMB
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 PHE 121 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1201 PRO* 1.3 70.5 - - - +
1221 SER* 1.3 65.3 + - - +
1241 VAL* 3.1 3.9 + - + +
1251 LYS* 2.9 56.7 + - + +
1351 VAL* 4.1 16.4 - - + -
1561 PHE* 3.3 36.9 - + + -
1571 LEU 3.5 22.0 - - - -
1591 ILE 5.1 0.2 - - - -
1601 THR* 3.7 19.5 - - + -
1621 GLU* 4.1 4.9 - - - -
1711 VAL* 3.7 26.2 - - + -
1951 CYS* 3.4 24.0 - - + -
2091 CYS* 3.0 21.3 + - + +
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Residues in contact with SER 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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1201 PRO* 4.3 2.9 - - - +
1211 PHE* 1.3 82.5 - - - +
1231 LYS* 1.3 82.2 + - - +
1251 LYS* 3.5 14.7 + - - +
1261 ALA* 3.0 28.9 + - - +
2091 CYS* 4.6 1.4 + - - +
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Residues in contact with LYS 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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1191 MET* 3.6 22.5 - - + +
1201 PRO* 2.9 42.8 + - + +
1221 SER* 1.3 88.1 + - - +
1241 VAL* 1.3 61.4 + - - +
1261 ALA* 3.4 5.6 + - - +
1271 LEU* 2.8 31.4 + - - +
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Residues in contact with VAL 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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1191 MET* 3.3 35.0 - - + +
1201 PRO 3.6 8.1 - - - +
1211 PHE* 3.1 7.4 + - + +
1231 LYS* 1.3 75.8 - - - +
1251 LYS* 1.3 58.6 + - - +
1271 LEU* 3.3 2.7 + - - +
1281 CYS* 2.9 44.5 + - - -
1351 VAL* 4.0 21.8 - - + -
1561 PHE* 4.1 15.7 - - + +
2131 LYS 4.4 0.9 - - - +
2141 THR 4.8 1.3 - - - +
2151 ALA* 3.7 30.7 - - + -
2161 VAL 4.3 2.0 - - - +
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Residues in contact with LYS 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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1211 PHE* 2.9 49.2 + - + +
1221 SER* 3.7 11.5 - - - +
1241 VAL* 1.3 77.7 - - - +
1261 ALA* 1.3 61.8 + - - +
1281 CYS* 3.6 1.0 + - - +
1291 SER* 3.0 34.4 + - - +
1351 VAL* 3.6 19.1 - - + -
1621 GLU* 4.2 10.9 + - - -
1711 VAL* 4.6 14.3 - - + +
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Residues in contact with ALA 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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1221 SER 3.0 18.3 + - - +
1231 LYS* 3.7 6.1 - - - +
1241 VAL 3.3 0.2 - - - -
1251 LYS* 1.3 75.8 - - - +
1271 LEU* 1.3 63.8 + - - +
1291 SER* 3.3 5.2 + - - -
1301 GLU* 3.0 25.7 + - - +
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Residues in contact with LEU 127 (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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1151 ASN* 4.8 3.4 - - - +
1171 GLU* 5.1 1.3 - - - +
1191 MET* 3.9 26.7 - - + -
1231 LYS 2.8 18.4 + - - +
1241 VAL 3.7 4.0 - - - +
1261 ALA* 1.3 75.8 - - - +
1281 CYS* 1.3 63.9 + - - +
1301 GLU* 3.1 32.5 + - - +
1311 LEU* 3.2 27.1 + - + +
2151 ALA* 4.6 4.5 - - + -
2171 CYS* 5.1 1.8 - - - -
1013 PHE* 3.7 34.3 - - + -
1073 SER* 6.2 2.7 - - - -
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Residues in contact with CYS 128 (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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1241 VAL* 2.9 39.6 + - - +
1251 LYS 4.1 2.5 - - - +
1271 LEU* 1.3 74.1 - - - +
1291 SER* 1.3 57.0 + - - +
1311 LEU* 2.9 15.2 + - - +
1331 GLY* 2.9 24.7 + - - -
1341 THR* 3.7 25.8 - - - -
1351 VAL* 3.9 2.7 - - - +
2161 VAL 4.0 1.6 - - - -
2171 CYS* 2.0 57.7 - - + -
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Residues in contact with SER 129 (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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1251 LYS* 3.0 25.0 + - - +
1261 ALA* 3.7 6.1 - - - -
1281 CYS* 1.3 77.7 - - - +
1301 GLU* 1.3 57.0 + - - +
1321 ARG* 3.0 24.9 + - - +
1331 GLY 3.6 11.1 + - - -
1341 THR* 5.5 1.6 - - - -
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Residues in contact with GLU 130 (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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1261 ALA 3.0 12.6 + - - +
1271 LEU* 3.2 30.7 - - - +
1291 SER* 1.3 76.6 - - - +
1311 LEU* 1.3 60.1 + - + +
1321 ARG* 3.3 2.4 + - - +
943 LEU* 3.1 18.7 - - - +
973 LYS* 3.8 33.1 + - + +
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Residues in contact with LEU 131 (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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1271 LEU* 3.2 23.8 + - + +
1281 CYS 2.9 8.3 + - - +
1301 GLU* 1.3 82.3 - - + +
1321 ARG* 1.3 70.8 + - - +
1331 GLY 3.3 0.2 - - - -
2171 CYS* 4.4 7.4 - - - -
2191 PHE* 3.3 23.9 - - + -
943 LEU* 3.7 11.7 - - + +
973 LYS* 3.9 18.6 - - + +
983 LEU* 3.8 40.8 - - + +
1013 PHE* 3.7 41.5 - - + -
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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