Contacts of the helix formed by residues 1527 - 1538 (chain A) in PDB entry 6FF7
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 ASN1527 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1255A THR* 4.8 9.1 - - - -
1525A GLY 4.0 0.6 + - - -
1526A LEU* 1.3 76.0 - - - +
1528A GLN* 1.3 64.2 + - - +
1529A ILE* 3.4 4.5 - - + +
1530A PRO* 4.3 12.0 - - + +
1531A ASN* 4.3 8.7 + - - +
215t ASP* 4.2 12.3 - - + -
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Residues in contact with GLN1528 (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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1526A LEU 3.6 1.7 + - - +
1527A ASN* 1.3 72.5 - - - +
1529A ILE* 1.3 60.0 + - - +
1530A PRO 3.5 0.2 - - - -
1531A ASN* 3.3 8.7 + - - +
1532A ARG* 2.9 30.0 + - - +
215t ASP* 3.2 21.8 + - - +
216t SER 4.8 3.4 - - - +
217t CYS 3.7 20.4 - - - +
218t LYS* 4.8 6.5 - - - +
219t PHE 5.9 0.2 - - - +
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Residues in contact with ILE1529 (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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1527A ASN* 3.4 3.4 - - + +
1528A GLN* 1.3 76.1 - - - +
1530A PRO* 1.4 59.3 - - - +
1532A ARG* 4.3 4.8 - - - +
1533A ARG* 2.9 29.6 + - - +
215t ASP* 4.8 4.7 + - + +
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Residues in contact with PRO1530 (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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1255A THR* 5.1 11.0 - - - -
1527A ASN* 4.3 11.6 - - + +
1528A GLN 3.5 0.4 - - - -
1529A ILE* 1.4 76.1 - - - +
1531A ASN* 1.3 58.1 + - - +
1533A ARG* 4.3 4.0 - - + +
1534A PHE* 2.9 33.4 + - - +
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Residues in contact with ASN1531 (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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1255A THR* 4.8 14.5 - - - -
1256A PHE* 5.8 2.9 - - + +
1527A ASN 4.3 7.7 + - - +
1528A GLN* 3.3 14.1 + - - +
1530A PRO* 1.3 78.6 - - - +
1532A ARG* 1.3 59.3 + - - +
1534A PHE* 4.3 4.0 - - - +
1535A THR* 3.6 19.2 + - - -
1568A THR* 4.9 6.6 - - - -
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Residues in contact with ARG1532 (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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1528A GLN* 2.9 16.1 + - + +
1529A ILE* 4.3 4.0 - - - +
1531A ASN* 1.3 78.5 - - - +
1533A ARG* 1.3 59.6 + - - +
1534A PHE 3.3 0.4 - - - -
1535A THR* 3.4 2.9 + - - -
1536A LEU* 2.9 23.0 + - - +
1568A THR* 4.7 8.7 - - - +
1571A ILE* 5.7 1.8 - - + -
1572A SER* 3.3 30.4 - - - +
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Residues in contact with ARG1533 (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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1529A ILE 2.9 18.8 + - - +
1530A PRO* 4.3 4.0 - - + +
1532A ARG* 1.3 73.9 - - - +
1534A PHE* 1.3 60.6 + - - +
1536A LEU* 3.3 5.8 + - - +
1537A TRP* 2.9 27.7 + - - +
1750A GLY 3.5 24.9 - - - +
1751A LEU* 4.2 18.6 - - - +
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Residues in contact with PHE1534 (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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1256A PHE* 6.4 2.2 - - + -
1324A GLY 6.0 2.0 - - - +
1530A PRO 2.9 18.8 + - - +
1531A ASN* 4.6 4.0 - - - +
1533A ARG* 1.3 74.5 - - - +
1535A THR* 1.3 64.7 + - - +
1537A TRP* 3.2 16.0 + - - +
1538A TRP* 3.5 13.5 + - - +
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Residues in contact with THR1535 (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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1531A ASN 3.6 17.8 + - - -
1532A ARG* 3.4 7.3 + - - -
1534A PHE* 1.3 77.1 - - - +
1536A LEU* 1.3 61.7 + - - +
1537A TRP 3.5 0.2 + - - -
1538A TRP* 3.8 8.6 + - - +
1539A SER* 3.8 12.3 + - - -
1542A ILE* 5.1 5.2 - - - +
1568A THR* 4.8 6.7 - - - -
1569A LEU* 4.7 28.6 - - - +
1572A SER* 5.0 0.9 - - - -
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Residues in contact with LEU1536 (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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1532A ARG 2.9 18.3 + - - +
1533A ARG* 3.5 9.9 - - - +
1534A PHE 3.2 0.2 - - - -
1535A THR* 1.3 79.4 - - - +
1537A TRP* 1.3 60.4 + - - +
1539A SER* 3.4 20.3 - - - -
1572A SER* 4.1 21.0 - - - +
1750A GLY 4.9 7.4 - - - +
1751A LEU* 5.5 7.0 - - + -
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Residues in contact with TRP1537 (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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1487A HIS* 3.3 27.7 - - - +
1488A THR 4.7 1.6 + - - -
1533A ARG 2.9 16.9 + - - +
1534A PHE* 3.2 11.1 + - - +
1536A LEU* 1.3 79.5 - - - +
1538A TRP* 1.3 56.6 + - + +
1539A SER 3.3 2.5 + - - -
1751A LEU* 6.3 3.6 - - + -
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Residues in contact with TRP1538 (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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1315A VAL* 5.6 11.4 - - + -
1486A GLU* 5.6 3.4 - - + -
1487A HIS* 5.2 5.2 - - - +
1534A PHE 3.5 10.5 + - - +
1535A THR* 3.8 4.7 + - - +
1536A LEU 3.4 0.2 - - - -
1537A TRP* 1.3 75.2 - - - +
1539A SER* 1.3 56.8 + - - +
1540A PRO 3.6 2.2 - - - -
1541A THR* 3.3 13.1 + - - +
1542A ILE* 3.0 31.6 + - + +
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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