Contacts of the strand formed by residues 1042 - 1048 (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 THR1042 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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995B VAL* 4.6 2.0 - - + -
1035B ILE* 3.6 24.0 - - + -
1036B VAL 3.3 11.0 - - - +
1037B SER* 2.9 19.1 + - - +
1041B GLN* 1.3 76.3 + - - +
1043B PHE* 1.3 69.3 + - - +
1109B ARG* 4.1 24.6 + - - +
1137B GLY* 3.4 17.9 - - - -
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Residues in contact with PHE1043 (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* 4.8 4.3 - - + -
1035B ILE* 3.6 7.8 - - - +
1036B VAL* 2.8 55.0 + - + +
1038B THR* 4.1 18.8 - - + -
1041B GLN* 4.1 16.6 - - + -
1042B THR* 1.3 83.8 - - - +
1044B LEU* 1.3 65.3 + - - +
1054B THR* 3.2 33.2 - - + -
1055B VAL* 4.2 7.2 - - + -
1058B GLY* 3.3 35.2 - - - -
1059B ALA* 3.5 16.2 - - + -
1137B GLY* 3.1 18.6 - - - +
1139B ALA* 3.6 13.5 - - + +
7C CYS* 4.9 3.6 - - - +
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Residues in contact with LEU1044 (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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998B ILE* 4.0 7.9 - - + -
1033B VAL* 4.2 11.4 - - + -
1034B GLN 3.3 13.2 - - - +
1035B ILE* 3.7 21.3 - - + -
1036B VAL* 4.1 2.9 - - - -
1043B PHE* 1.3 88.2 - - - +
1045B ALA* 1.3 56.3 + - - +
1054B THR* 2.6 28.9 + - - -
1107B VAL 3.9 10.1 - - - +
1108B THR 3.9 2.5 - - - +
1109B ARG* 3.7 34.8 - - + +
1137B GLY 3.8 8.1 - - - +
1138B SER* 3.7 14.6 - - - +
1139B ALA 3.0 4.2 + - - +
1140B GLY* 3.2 9.3 - - - -
1141B GLY* 3.6 26.7 - - - +
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Residues in contact with ALA1045 (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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1032B GLU 3.8 0.9 - - - +
1033B VAL* 3.5 3.1 - - - +
1034B GLN* 2.7 39.4 + - + +
1036B VAL* 4.1 21.1 - - + +
1044B LEU* 1.3 76.0 - - - +
1046B THR* 1.3 62.7 + - - +
1052B LEU* 3.6 23.6 - - + -
1053B TRP 3.2 14.6 - - - +
1054B THR* 3.9 10.1 - - + -
1085B TRP* 4.9 1.6 - - + -
1140B GLY 3.7 1.1 - - - -
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Residues in contact with THR1046 (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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1032B GLU 3.4 7.2 - - - +
1033B VAL* 4.2 5.3 - - + +
1045B ALA* 1.3 74.7 + - - +
1047B SER* 1.3 66.2 + - - +
1048B ILE* 4.1 8.3 - - + -
1052B LEU* 3.8 3.1 - - - -
1053B TRP* 2.9 36.1 + - - +
1094B LEU* 3.5 31.4 - - + -
1140B GLY 2.7 22.1 + - - -
1141B GLY* 3.5 12.6 - - - -
1142B PRO* 3.5 14.9 - - + +
1153B ILE* 3.7 12.3 - - + -
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Residues in contact with SER1047 (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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1031B GLY 4.9 0.5 + - - -
1032B GLU 2.9 12.5 + - - +
1034B GLN* 5.7 0.5 - - - +
1046B THR* 1.3 70.7 - - - +
1048B ILE* 1.3 62.6 + - - +
1051B VAL 3.2 8.7 - - - -
1052B LEU* 3.4 17.5 - - - +
1087B ALA* 3.8 19.0 - - - +
1088B PRO* 4.6 0.2 - - - +
1091B SER* 3.8 9.6 + - - -
1092B ARG 3.4 22.6 - - - +
1093B SER* 3.3 11.8 - - - -
1094B LEU* 2.9 27.2 + - - +
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Residues in contact with ILE1048 (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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1046B THR* 3.7 10.9 + - + -
1047B SER* 1.3 79.9 - - - +
1049B ASN* 1.3 91.2 + - - +
1050B GLY 3.2 2.0 + - - -
1051B VAL* 3.0 10.1 + - - +
1053B TRP* 3.1 27.1 + - + +
1093B SER* 3.9 3.8 - - - -
1094B LEU* 3.7 14.6 - - + +
1096B PRO* 4.3 11.7 - - + -
1142B PRO* 5.9 0.2 - - + -
1150B ALA* 3.8 27.8 - - + -
1152B GLY 5.1 1.8 - - - +
1153B ILE* 3.9 21.3 - - + -
1172B VAL* 4.3 8.1 - - + -
1175B LEU* 3.7 25.1 - - + -
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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