Contacts of the strand formed by residues 1119 - 1124 (chain A) in PDB entry 3MPX
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 THR1119 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1118A GLY* 1.3 71.8 - - - -
1120A LEU* 1.3 80.8 + - - +
1121A MSE 5.3 2.5 - - - -
1130A PRO* 4.0 22.9 - - + -
1131A ARG 3.4 14.4 - - - +
1132A HIS* 2.7 27.2 + - - +
1145A PRO* 4.4 9.4 - - + +
1194A GLU* 4.7 6.9 - - - -
1198A TRP* 5.3 0.5 + - - -
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Residues in contact with LEU1120 (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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1118A GLY 4.1 0.4 + - - +
1119A THR* 1.3 83.0 - - - +
1121A MSE 1.3 62.4 + - - +
1130A PRO* 3.6 2.4 - - - +
1131A ARG* 2.8 38.8 + - - +
1133A LEU* 3.8 26.9 - - + -
1176A LEU* 3.9 26.2 - - + -
1187A LEU* 4.0 20.6 - - + -
1188A SER 3.8 4.7 - - - +
1189A ALA* 3.9 28.9 - - + +
1194A GLU* 4.0 14.4 - - - -
1198A TRP* 4.1 25.1 - - + +
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Residues in contact with MSE1121 (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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1119A THR* 5.3 2.7 - - - -
1120A LEU* 1.3 74.8 - - - +
1122A LYS* 1.3 61.8 + - - +
1123A VAL* 3.6 1.7 + - + +
1128A ARG* 3.4 46.7 - - + +
1129A ARG 3.5 1.1 - - - +
1130A PRO* 3.7 31.6 - - + -
1187A LEU* 3.2 8.7 - - - -
1188A SER* 2.8 51.6 + - - +
1189A ALA 5.9 1.3 - - - +
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Residues in contact with LYS1122 (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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1120A LEU 3.9 1.4 + - - -
1121A MSE 1.3 70.1 - - - +
1123A VAL* 1.3 59.7 + - - +
1124A THR* 3.5 7.6 + - - -
1127A ASN 3.6 0.3 - - - +
1128A ARG* 3.5 6.5 - - - -
1129A ARG* 2.6 38.6 + - + +
1131A ARG* 3.7 30.9 - - + +
1142A TYR* 3.8 11.2 - - - +
1186A MSE 3.7 6.3 - - - +
1187A LEU* 4.2 2.9 - - + -
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Residues in contact with VAL1123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1121A MSE 4.0 2.2 - - + +
1122A LYS* 1.3 70.1 - - - +
1124A THR* 1.4 58.5 + - - +
1125A GLY 3.7 19.6 + - - +
1126A LYS* 5.3 2.9 - - - +
1127A ASN 3.8 8.7 - - - +
1128A ARG* 5.1 3.1 - - + +
1171A LYS 5.4 1.6 - - - +
1172A VAL* 3.6 46.9 - - + -
1186A MSE 3.0 38.6 + - + +
1188A SER* 3.8 20.0 - - - +
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Residues in contact with THR1124 (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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1122A LYS* 3.5 6.0 + - - -
1123A VAL* 1.4 70.2 - - - +
1125A GLY* 1.3 57.8 + - - +
1126A LYS 3.2 0.2 + - - -
1127A ASN* 3.1 39.1 + - - +
1129A ARG* 6.5 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