Contacts of the strand formed by residues 1549 - 1553 (chain B) in PDB entry 6X34
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 PHE1549 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1290B ARG* 3.5 57.2 - - + -
1291B LEU 4.9 4.3 - - - +
1292B SER 4.6 7.4 - - - -
1293B LEU 4.5 4.3 - - - -
1294B PRO* 3.5 35.7 - - + -
1452B TRP* 3.2 3.5 - - - -
1453B VAL* 2.5 46.7 + - + +
1455B PRO* 3.7 34.3 - - + -
1547B LYS* 5.2 5.4 - - + -
1548B LEU* 1.3 87.9 - - - +
1550B PRO* 1.3 71.5 - - + +
1551B ALA 3.1 0.9 + - - -
1643B GLU 3.3 22.4 - - - -
1644B GLU* 5.3 1.6 - - - -
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Residues in contact with PRO1550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1290B ARG* 4.1 0.6 - - - -
1291B LEU* 3.3 53.4 + - + +
1293B LEU 4.6 9.4 - - - +
1295B VAL* 5.4 0.9 - - + -
1435B TYR* 3.8 34.3 - - + +
1451B GLY 3.6 7.9 - - - +
1452B TRP* 3.5 30.7 - - + -
1548B LEU 4.4 1.3 - - - +
1549B PHE* 1.3 82.9 - - + +
1551B ALA* 1.3 58.0 + - - +
1552B VAL* 4.4 1.4 + - - +
1564B PHE* 5.4 0.2 - - - -
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Residues in contact with ALA1551 (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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1245B PHE* 6.2 0.2 - - + -
1289B LEU 3.4 19.7 - - - +
1290B ARG* 4.7 0.4 - - - -
1435B TYR* 6.1 0.2 - - - -
1449B TRP 4.2 0.4 - - - +
1450B VAL* 3.7 0.7 - - - +
1451B GLY 2.8 35.6 + - - +
1452B TRP 5.0 0.2 - - - -
1453B VAL* 3.6 28.0 - - + +
1493B TYR 5.9 0.2 - - - +
1549B PHE 3.1 1.6 + - - -
1550B PRO* 1.3 73.0 - - - +
1552B VAL* 1.3 67.7 + - - +
1553B PHE* 3.7 23.0 - - + -
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Residues in contact with VAL1552 (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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1289B LEU* 3.4 35.2 + - + +
1435B TYR* 4.7 8.5 - - + +
1437B VAL* 4.4 11.2 - - + -
1448B VAL* 5.2 2.5 - - + -
1449B TRP 3.5 2.9 - - - -
1450B VAL* 3.8 33.2 - - + -
1550B PRO 5.4 0.7 - - - +
1551B ALA* 1.3 80.6 - - - +
1553B PHE* 1.3 77.7 + - - +
1554B VAL* 4.9 2.7 - - + +
1562B ILE* 4.3 24.2 - - + -
1564B PHE* 3.9 28.4 - - + -
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Residues in contact with PHE1553 (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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1245B PHE* 5.9 2.2 - + - -
1287B LEU 5.0 3.8 - - - +
1288B PHE* 3.4 52.3 - + + -
1289B LEU* 4.2 4.0 - - - -
1447B CYS 3.5 2.5 - - - +
1448B VAL* 3.2 5.5 - - - +
1449B TRP* 2.7 74.0 + + + +
1451B GLY 5.6 0.2 - - - -
1453B VAL* 5.2 7.9 - - + -
1457B TYR* 5.3 12.3 - + - -
1464B PHE* 5.4 4.7 - - + -
1492B CYS* 5.9 5.8 - - + -
1493B TYR 4.8 12.8 - - - -
1494B MET* 4.9 4.7 - - + -
1551B ALA* 3.7 31.6 - - + -
1552B VAL* 1.3 77.6 - - - +
1554B VAL* 1.3 61.5 + - - +
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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