Contacts of the strand formed by residues 1113 - 1120 (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 VAL1113 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1000B LEU* 5.2 2.2 - - + -
1005B ALA* 4.0 24.7 - - + -
1105B TYR* 3.8 35.6 - - + -
1106B LEU 3.4 4.3 - - - +
1107B VAL* 4.6 13.9 - - + -
1111B ALA 3.9 0.6 + - - +
1112B ASP* 1.3 79.6 - - - +
1114B ILE* 1.3 62.1 + - - +
1115B PRO* 3.7 7.3 - - - +
1130B ARG* 4.8 4.0 + - - -
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Residues in contact with ILE1114 (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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1105B TYR* 3.5 2.6 - - - -
1106B LEU* 2.8 44.0 + - + +
1108B THR* 3.6 30.3 - - + -
1112B ASP* 4.3 9.9 - - + +
1113B VAL* 1.3 74.6 - - - +
1115B PRO* 1.3 78.4 - - + +
1116B VAL* 3.5 6.4 + - + +
1126B LEU* 4.1 24.7 - - + -
1128B SER 5.0 1.8 - - - +
1130B ARG* 4.1 28.9 - - + +
1134B TYR* 4.9 4.0 - - + -
1135B LEU* 3.9 26.5 - - + -
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Residues in contact with PRO1115 (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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1104B LEU 3.4 7.4 - - - +
1105B TYR* 4.1 19.7 - - + -
1113B VAL 3.7 8.0 - - - +
1114B ILE* 1.3 93.7 - - + +
1116B VAL* 1.3 63.0 + - - +
1126B LEU* 3.9 0.7 - - - -
1127B LEU* 3.3 42.0 + - + -
1128B SER* 4.7 8.6 + - - +
1130B ARG* 4.0 15.9 - - - +
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Residues in contact with VAL1116 (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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1102B SER 3.7 0.2 - - - +
1103B ASP* 3.8 1.6 - - - -
1104B LEU* 2.8 50.1 + - + +
1106B LEU* 4.4 14.4 - - + -
1114B ILE* 3.7 12.1 - - + +
1115B PRO* 1.3 79.4 - - - +
1117B ARG* 1.3 62.2 + - - +
1118B ARG 4.5 0.2 - - - +
1124B GLY* 3.6 27.6 - - - -
1125B SER 3.3 9.2 - - - +
1126B LEU* 4.5 15.5 - - + -
1127B LEU* 4.0 5.6 - - - +
1143B LEU* 4.2 10.5 - - + -
1167B VAL* 3.8 21.8 - - + -
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Residues in contact with ARG1117 (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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1102B SER* 3.6 7.0 - - - +
1103B ASP* 5.2 2.9 - - - +
1116B VAL* 1.3 71.2 - - - +
1118B ARG* 1.3 67.2 + - - +
1119B ARG* 3.4 14.4 + - - +
1124B GLY* 3.1 0.5 - - - -
1125B SER* 2.8 39.2 + - - +
1127B LEU* 3.6 29.0 - - + +
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Residues in contact with ARG1118 (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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1100B GLY 6.3 0.2 - - - -
1101B SER 4.8 12.2 + - - -
1102B SER* 2.8 37.5 + - - +
1104B LEU* 3.7 22.0 - - + +
1116B VAL 3.7 2.2 + - - -
1117B ARG* 1.3 74.3 - - - +
1119B ARG* 1.3 63.7 + - - +
1120B GLY 2.9 23.7 + - - +
1121B ASP* 2.7 39.5 + - - +
1123B ARG 3.7 7.9 - - - +
1124B GLY* 4.2 1.6 - - - -
1151B VAL* 3.7 22.1 - - - +
1169B PHE* 3.8 9.0 - - + -
1171B PRO* 4.5 6.5 - - - +
1173B GLU* 4.6 9.7 + - - -
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Residues in contact with ARG1119 (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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1117B ARG* 3.5 19.5 + - - +
1118B ARG* 1.3 81.1 - - - +
1120B GLY* 1.3 59.2 + - - +
1123B ARG* 2.8 20.3 + - + +
1124B GLY* 4.2 0.4 - - - -
1125B SER* 3.0 41.4 + - - +
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Residues in contact with GLY1120 (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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1118B ARG* 2.9 23.4 + - - +
1119B ARG* 1.3 78.5 - - - +
1121B ASP* 1.3 67.8 + - - -
1122B SER 3.2 3.4 + - - -
1123B ARG* 3.4 11.8 + - - +
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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