Contacts of the helix formed by residues 1170 - 1175 (chain B) in PDB entry 3DLS
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 ALA1170 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1169B CYS* 1.3 75.7 - - - +
1171B PRO* 1.4 73.7 - - + +
1172B GLU* 3.3 29.4 - - + +
1173B VAL* 3.1 12.7 + - + -
1174B LEU* 3.1 11.8 + - - +
1184B LEU* 3.4 23.1 - - + +
1187B TRP* 3.5 15.6 - - + -
1239B ARG* 3.7 11.2 - - - +
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Residues in contact with PRO1171 (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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1170B ALA* 1.4 86.8 - - + +
1172B GLU* 1.3 65.3 + - - +
1173B VAL 3.2 0.9 + - - -
1174B LEU* 3.4 6.7 + - + +
1175B MET* 3.3 29.4 + - - +
1187B TRP* 3.6 25.4 - - + -
1209B THR* 3.4 33.8 - - + +
1210B VAL* 3.8 25.1 - - + +
1234B PRO* 3.9 19.7 - - + +
1239B ARG* 3.8 1.3 - - - +
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Residues in contact with GLU1172 (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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1170B ALA* 3.3 16.8 - - - +
1171B PRO* 1.3 74.5 - - - +
1173B VAL* 1.3 68.6 + - + +
1175B MET* 3.8 5.1 + - - -
1177B ASN* 2.9 47.7 + - + +
1179B TYR* 5.9 2.0 - - + +
1183B GLU* 4.1 6.6 - - - +
1184B LEU* 4.3 3.6 + - - +
1234B PRO 3.8 3.8 + - - +
1236B PRO* 3.8 32.2 - - + +
1239B ARG* 3.0 43.2 + - - -
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Residues in contact with VAL1173 (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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985A LEU* 3.8 31.7 - - + +
1162B PHE* 4.1 15.0 - - + -
1169B CYS* 3.6 20.0 - - - -
1170B ALA 3.1 8.3 + - - +
1172B GLU* 1.3 89.5 - - + +
1174B LEU* 1.3 56.5 + - - +
1175B MET 3.0 5.2 - - - -
1176B GLY* 3.1 17.8 + - - -
1177B ASN 3.8 15.0 - - - +
1179B TYR* 3.9 23.3 - - + -
1184B LEU* 3.9 16.4 - - + -
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Residues in contact with LEU1174 (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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1010A PHE* 3.4 39.7 - - + +
1014A TRP* 5.0 0.7 - - - -
1166B ILE* 3.7 28.9 - - + +
1169B CYS* 3.5 40.2 - - + +
1170B ALA 3.1 12.8 + - - +
1171B PRO* 3.4 5.6 + - + +
1173B VAL* 1.3 75.1 - - - +
1175B MET* 1.3 58.9 + - - +
1176B GLY 3.3 1.5 + - - -
1206B LEU* 3.5 42.2 - - + +
1209B THR* 3.9 15.0 - - + +
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Residues in contact with MET1175 (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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987A GLY* 4.6 5.5 - - - -
1002A MET 4.1 11.7 - - - +
1003A SER* 4.5 2.0 - - - -
1004A PRO* 3.6 31.0 - - + -
1010A PHE* 3.6 11.9 - - + -
1014A TRP* 3.7 30.5 - - + -
1171B PRO 3.3 17.9 + - - +
1172B GLU* 4.0 8.1 - - - +
1173B VAL 3.0 1.4 - - - -
1174B LEU* 1.3 77.4 - - - +
1176B GLY* 1.3 58.1 + - - +
1177B ASN* 3.4 15.4 + - - +
1210B VAL* 3.7 28.9 - - + -
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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