Contacts of the strand formed by residues 1033 - 1037 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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997B ARG* 3.3 8.7 - - - +
998B ILE* 2.9 59.2 + - + +
1000B LEU* 4.0 18.8 - - + -
1031B GLY 5.3 0.2 - - - -
1032B GLU* 1.3 85.9 + - + +
1034B GLN* 1.3 67.3 + - - +
1044B LEU* 4.2 11.4 - - + -
1045B ALA 3.5 7.2 - - - +
1046B THR* 4.2 7.4 - - + +
1094B LEU* 4.8 1.3 - - + -
1107B VAL* 5.2 1.8 - - + -
1142B PRO* 3.8 38.1 - - + -
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Residues in contact with GLN1034 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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994B ILE* 3.5 30.5 - - + +
996B GLY 3.3 15.3 + - - +
997B ARG* 3.7 11.3 - - - +
1029B VAL* 3.4 20.4 - - + +
1030B GLU 3.0 22.2 + - - +
1031B GLY 3.3 17.2 - - - +
1032B GLU 4.3 1.1 - - - +
1033B VAL* 1.3 76.0 + - - +
1035B ILE* 1.3 62.5 + - - +
1036B VAL* 3.9 12.1 - - + -
1044B LEU* 3.3 9.0 - - - +
1045B ALA* 2.7 38.5 + - + +
1047B SER* 5.7 0.6 + - - +
1052B LEU* 4.1 19.7 - - + -
1088B PRO* 5.3 1.1 - - + -
1091B SER* 4.9 0.6 - - - -
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Residues in contact with ILE1035 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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994B ILE* 3.5 4.9 - - - +
995B VAL* 2.8 39.2 + - + -
996B GLY* 2.9 17.9 + - - +
997B ARG* 3.7 33.2 - - - +
998B ILE* 3.9 12.3 - - + -
1007B ALA* 4.3 7.0 - - + -
1008B GLN 4.0 9.2 - - - +
1009B GLN* 5.7 0.9 - - - -
1034B GLN* 1.3 71.7 - - - +
1036B VAL* 1.3 58.9 + - - +
1042B THR* 3.6 26.9 - - + -
1043B PHE 3.6 6.3 - - - +
1044B LEU* 3.7 17.0 - - + -
1109B ARG* 4.2 23.6 - - + +
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Residues in contact with VAL1036 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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992B VAL* 3.6 18.2 - - + -
993B VAL 3.2 9.2 - - - +
994B ILE* 4.1 19.3 - - + -
995B VAL* 4.4 0.2 - - - -
1034B GLN* 4.3 3.8 - - + -
1035B ILE* 1.3 78.4 - - - +
1037B SER* 1.3 65.9 + - - +
1042B THR* 3.3 2.1 - - - +
1043B PHE* 2.8 77.9 + - + +
1044B LEU 4.1 7.0 - - - +
1045B ALA* 4.1 21.5 - - + -
1054B THR* 5.3 0.7 - - + -
1064B ILE* 4.7 4.5 - - + -
1085B TRP* 5.9 0.4 - - + -
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Residues in contact with SER1037 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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991B SER 4.3 1.4 - - - +
992B VAL* 3.6 5.6 - - - -
993B VAL* 2.9 32.7 + - - +
995B VAL* 3.4 18.4 - - - +
1016B CYS* 3.8 23.3 - - - -
1020B SER* 6.0 0.2 - - - -
1036B VAL* 1.3 76.3 + - - +
1038B THR* 1.3 70.9 + - - +
1041B GLN 3.3 5.6 - - - -
1042B THR* 2.9 21.6 + - - +
1043B PHE* 4.8 1.1 - - - -
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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