Contacts of the strand formed by residues 1033 - 1037 (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 VAL1033 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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997A ARG* 3.4 9.2 + - - +
998A ILE* 3.0 59.4 + - + +
1000A LEU* 4.0 17.9 - - + -
1032A GLU* 1.3 86.4 + - + +
1034A GLN* 1.3 69.8 + - - +
1044A LEU* 4.4 10.8 - - + -
1045A ALA 3.5 7.2 - - - +
1046A THR* 4.2 7.6 - - + +
1094A LEU* 5.1 1.6 - - + -
1107A VAL* 5.0 0.9 - - + -
1142A PRO* 3.8 39.0 - - + -
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Residues in contact with GLN1034 (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* 3.5 30.0 - - + +
996A GLY 3.4 14.5 - - - +
997A ARG* 4.0 3.6 - - - +
1029A VAL* 3.5 21.4 - - + +
1030A GLU 2.9 27.2 + - - +
1031A GLY 3.4 19.0 + - - -
1032A GLU 4.4 0.8 - - - +
1033A VAL* 1.3 76.8 - - - +
1035A ILE* 1.3 62.6 + - - +
1036A VAL* 3.9 12.6 - - + -
1044A LEU* 3.2 9.6 - - - +
1045A ALA* 2.8 33.4 + - + +
1052A LEU* 4.1 20.0 - - + -
1088A PRO* 5.6 0.7 - - + -
1091A SER* 4.8 2.2 - - - -
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Residues in contact with ILE1035 (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* 3.5 3.8 - - - -
995A VAL* 2.8 33.2 + - + -
996A GLY* 2.8 17.0 + - - +
997A ARG* 3.8 26.5 - - - +
998A ILE* 3.8 16.4 - - + -
1007A ALA* 4.2 11.7 - - + -
1008A GLN 4.2 6.5 - - - +
1009A GLN* 5.9 0.4 - - - -
1034A GLN* 1.3 72.5 - - - +
1036A VAL* 1.3 59.1 + - - +
1042A THR* 3.5 30.7 - - + -
1043A PHE 3.4 7.2 - - - +
1044A LEU* 3.7 17.5 - - + -
1109A ARG* 4.4 11.9 - - + +
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Residues in contact with VAL1036 (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* 3.5 21.3 - - + -
993A VAL 3.2 4.3 - - - +
994A ILE* 4.0 21.3 - - + -
995A VAL* 4.4 1.6 - - - -
1034A GLN* 4.3 3.4 - - + -
1035A ILE* 1.3 79.7 - - - +
1037A SER* 1.3 61.6 + - - +
1042A THR* 3.3 4.5 - - - +
1043A PHE* 2.8 75.9 + - + +
1044A LEU 4.2 6.3 - - - +
1045A ALA* 4.0 22.0 - - + -
1052A LEU* 5.2 0.2 - - + -
1054A THR* 5.4 0.7 - - + -
1064A ILE* 4.9 3.8 - - + -
1085A TRP* 5.8 0.9 - - + -
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Residues in contact with SER1037 (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 SER 4.2 1.6 - - - +
992A VAL* 3.6 4.9 - - - -
993A VAL* 2.9 34.2 + - - +
995A VAL* 4.1 23.8 - - - -
1016A CYS* 4.1 10.6 - - - -
1020A SER* 5.8 0.3 - - - -
1036A VAL* 1.3 76.2 - - - +
1038A THR* 1.3 83.1 + - - +
1041A GLN 3.2 9.3 + - - -
1042A THR* 3.3 15.8 + - - -
1043A PHE* 4.9 0.7 - - - -
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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