Contacts of the helix formed by residues 995 - 1002 (chain A) in PDB entry 3LXK
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 ALA 995 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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993A TRP 3.6 1.0 + - - -
994A TYR* 1.3 74.3 - - - +
996A PRO* 1.3 77.2 - - + +
997A GLU* 3.2 25.6 - - - +
998A SER* 2.9 16.5 + - - +
999A LEU* 3.1 10.6 + - - +
1008A SER* 3.8 15.0 + - - +
1011A TRP* 3.5 30.3 - - + -
1012A SER* 5.0 1.4 + - - -
1085A ARG* 3.9 1.1 - - - +
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Residues in contact with PRO 996 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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994A TYR 3.8 0.4 - - - -
995A ALA* 1.3 88.2 - - + +
997A GLU* 1.3 60.9 - - - +
999A LEU* 3.2 10.1 + - + +
1000A SER* 2.8 33.6 + - - -
1011A TRP* 3.5 38.6 - - + -
1051A LEU* 4.1 20.5 - - + +
1054A LEU* 4.5 12.6 - - + +
1055A GLU* 5.5 4.3 - - + -
1059A ARG* 5.6 0.7 - - - +
1080A PRO* 4.3 16.4 - - + +
1085A ARG* 3.8 1.3 - - - +
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Residues in contact with GLU 997 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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995A ALA* 3.5 12.7 - - - +
996A PRO* 1.3 75.6 - - - +
998A SER* 1.3 58.9 + - - +
1000A SER* 3.4 9.4 - - - -
1001A ASP* 3.0 23.4 + - - +
1003A ILE* 3.3 43.3 + - + +
1005A SER* 4.8 1.7 + - - -
1008A SER* 3.7 9.9 + - - -
1080A PRO 4.3 1.0 - - - +
1082A PRO* 3.8 24.5 - - + +
1085A ARG* 2.8 45.4 + - - -
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Residues in contact with SER 998 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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994A TYR* 4.3 8.3 - - - -
995A ALA* 2.9 16.8 + - - +
997A GLU* 1.3 77.1 - - - +
999A LEU* 1.3 61.9 + - - +
1002A ASN* 2.9 28.1 + - - +
1003A ILE 2.6 26.3 + - - +
1004A PHE* 3.6 32.6 - - - -
1008A SER* 3.9 14.0 - - - -
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Residues in contact with LEU 999 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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991A ILE* 4.0 13.2 - - + +
994A TYR* 3.6 39.9 - - + +
995A ALA 3.1 13.4 + - - +
996A PRO* 3.5 5.6 - - + +
998A SER* 1.3 78.5 - - - +
1000A SER* 1.3 62.0 + - - +
1002A ASN* 4.6 4.9 - - - +
1047A LEU* 3.8 43.8 - - + +
1050A LEU* 4.2 16.6 - - + -
1051A LEU* 4.1 22.4 - - + +
1054A LEU* 4.0 27.1 - - + -
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Residues in contact with SER1000 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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996A PRO 2.8 23.1 + - - -
997A GLU* 3.4 9.0 - - - +
999A LEU* 1.3 75.9 - - - +
1001A ASP* 1.3 84.9 + - - +
1002A ASN* 3.8 2.2 + - - -
1051A LEU* 3.7 24.7 - - - -
1055A GLU* 5.0 3.4 - - - -
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Residues in contact with ASP1001 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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982A VAL* 3.6 12.8 - - - +
997A GLU* 3.0 12.4 + - - +
1000A SER* 1.3 100.6 + - - +
1002A ASN* 1.3 77.9 + - - +
1003A ILE* 3.0 21.7 + - + +
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Residues in contact with ASN1002 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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982A VAL* 3.3 4.1 - - + +
983A VAL* 3.1 48.9 + - + +
984A ARG 4.2 5.5 + - - -
985A GLU 3.8 18.8 + - - -
986A PRO* 3.7 24.6 - - - +
987A GLY 4.8 1.0 + - - -
998A SER* 2.9 21.9 + - - +
999A LEU 4.6 4.9 - - - +
1000A SER 5.3 1.8 + - - -
1001A ASP* 1.3 81.0 + - - +
1003A ILE* 1.3 60.0 + - - +
1004A PHE* 3.7 13.9 - - + -
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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