Contacts of the strand formed by residues 993 - 999 (chain A) in PDB entry 3M5M
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 993 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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991A SER 3.6 2.9 - - - +
992A VAL* 1.3 78.6 - - - +
994A ILE* 1.3 77.0 + - - +
995A VAL* 3.4 8.3 + - + +
1011A ARG* 3.9 15.9 - - - +
1016A CYS* 3.6 20.6 - - - +
1019A THR* 3.8 24.7 - - + +
1020A SER* 3.4 40.4 - - - +
1025A ASP* 5.1 1.8 - - - +
1036A VAL* 3.2 3.5 - - - -
1037A SER 2.9 35.0 + - - +
1065A ALA* 4.4 2.7 - - + -
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Residues in contact with ILE 994 (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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992A VAL 4.4 0.6 + - - -
993A VAL* 1.3 81.8 - - - +
995A VAL* 1.3 60.5 + - - +
996A GLY 3.7 12.3 - - - +
1010A THR* 4.3 7.4 + - - +
1011A ARG* 4.1 11.3 + - - +
1025A ASP* 4.3 17.4 + - - +
1027A ASN* 5.5 1.4 + - - +
1029A VAL* 3.7 28.3 - - + -
1034A GLN* 3.5 32.8 - - + +
1035A ILE 3.5 6.1 - - - +
1036A VAL* 4.0 16.6 - - + -
1052A LEU* 4.4 1.1 - - + -
1064A ILE* 4.2 19.2 - - + +
1065A ALA* 5.4 4.8 + - - +
1088A PRO* 4.0 20.2 - - + -
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Residues in contact with VAL 995 (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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993A VAL* 3.7 10.8 - - + +
994A ILE* 1.3 77.5 - - - +
996A GLY* 1.3 58.0 + - - +
1009A GLN* 3.4 10.8 - - + +
1010A THR* 2.8 26.0 + - - -
1011A ARG* 3.2 22.2 + - + +
1016A CYS* 3.5 37.5 - - + -
1035A ILE* 2.8 33.3 + - + +
1036A VAL 4.4 0.2 - - - -
1037A SER* 4.1 16.2 - - - -
1042A THR* 4.6 3.6 - - + -
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Residues in contact with GLY 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 ILE* 3.7 2.8 - - - +
995A VAL* 1.3 79.8 - - - +
997A ARG* 1.3 64.5 + - - +
1008A GLN 3.0 14.4 - - - -
1009A GLN* 4.1 0.4 - - - -
1010A THR* 3.3 15.4 + - - -
1034A GLN* 3.4 11.9 - - - +
1035A ILE* 2.8 30.5 + - - +
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Residues in contact with ARG 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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996A GLY* 1.3 77.0 - - - +
998A ILE* 1.3 68.7 + - - +
999A ASN* 3.8 41.8 + - - +
1000A LEU 4.6 0.4 - - - +
1001A SER* 4.1 2.2 + - - -
1007A ALA* 3.5 2.6 - - - -
1008A GLN* 2.9 59.4 + - + +
1010A THR* 5.0 8.7 - - + -
1030A GLU* 3.8 44.1 + - - +
1031A GLY* 3.6 17.4 - - - +
1032A GLU* 4.5 3.2 + - - -
1033A VAL 3.4 12.9 + - - +
1034A GLN* 4.0 8.3 - - - +
1035A ILE* 3.8 8.3 - - - +
1092A ARG* 4.0 13.7 - - - +
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Residues in contact with ILE 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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997A ARG* 1.3 79.2 + - - +
999A ASN* 1.3 63.2 + - - +
1000A LEU* 3.5 19.9 + - + +
1006A TYR 3.7 1.3 - - - +
1007A ALA* 3.9 11.4 - - + -
1032A GLU* 5.3 1.6 - - - +
1033A VAL* 3.0 43.0 + - + +
1035A ILE* 3.8 16.2 - - + -
1044A LEU* 3.9 11.9 - - + -
1107A VAL* 3.6 25.6 - - + -
1108A THR 3.7 12.3 - - - +
1109A ARG* 3.4 27.1 - - - +
1111A ALA* 4.2 17.5 - - + +
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Residues in contact with ASN 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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997A ARG* 3.8 24.8 - - - +
998A ILE* 1.3 71.7 - - - +
1000A LEU* 1.3 57.0 + - - +
1001A SER* 3.0 36.0 + - - -
1002A GLY 4.2 2.4 + - - -
1004A THR 3.9 1.6 - - - +
1005A ALA* 3.3 8.8 - - - +
1006A TYR* 2.9 70.0 + - + +
1008A GLN* 3.2 24.9 + - - +
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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