Contacts of the helix formed by residues 1464 - 1481 (chain r) 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 GLY1464 (chain r).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1458r LEU 3.9 9.6 - - - -
1459r ILE* 3.5 17.4 - - - -
1461r GLY 3.0 14.9 + - - -
1462r GLU* 2.9 6.5 + - - +
1463r ASN* 1.3 76.9 - - - +
1465r PRO* 1.4 66.4 - - - +
1466r VAL 3.1 2.0 - - - -
1467r LEU* 2.8 17.7 + - - +
1468r GLU* 2.9 12.7 + - - +
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Residues in contact with PRO1465 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1459r ILE 4.5 1.2 - - - -
1461r GLY 4.7 0.4 - - - -
1463r ASN* 3.7 1.9 - - - +
1464r GLY* 1.4 74.1 - - - +
1466r VAL* 1.3 57.3 - - - +
1468r GLU* 3.2 9.0 + - + +
1469r VAL* 2.8 32.2 + - - +
1727r HIS* 4.7 9.5 - - + +
1728r LEU* 4.3 21.1 - - + +
1731r CYS* 4.1 33.7 - - + +
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Residues in contact with VAL1466 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1429r PRO* 4.4 19.9 - - + +
1430r GLU* 5.2 6.1 - - + +
1433r ASP* 5.3 8.3 - - + +
1463r ASN* 4.3 13.3 + - + +
1464r GLY 3.1 0.8 - - - -
1465r PRO* 1.3 79.0 - - - +
1467r LEU* 1.3 62.8 + - - +
1469r VAL* 3.5 6.5 + - - +
1470r ILE* 3.0 24.6 + - - +
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Residues in contact with LEU1467 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1381r PRO* 5.7 8.5 - - + -
1429r PRO* 4.1 18.7 - - + +
1456r VAL* 6.6 0.2 - - - -
1458r LEU* 5.8 0.9 - - + -
1459r ILE* 5.2 9.6 - - + +
1463r ASN 4.1 6.9 + - - +
1464r GLY* 2.8 14.7 + - - +
1466r VAL* 1.3 79.1 - - - +
1468r GLU* 1.3 63.3 + - - +
1470r ILE* 3.1 5.0 + - - +
1471r CYS* 3.0 23.4 + - - +
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Residues in contact with GLU1468 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1459r ILE* 5.2 12.2 - - + +
1464r GLY 2.9 10.4 + - - +
1465r PRO* 3.4 12.8 - - + +
1467r LEU* 1.3 76.9 - - - +
1469r VAL* 1.3 56.5 + - - +
1471r CYS* 3.2 6.3 + - - +
1472r SER* 2.9 31.4 + - - -
1726r SER* 6.1 3.8 - - - -
1728r LEU* 5.6 8.1 - - + -
1758r THR* 6.3 2.5 - - - -
1759r PHE* 5.1 18.7 + - + +
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Residues in contact with VAL1469 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1465r PRO 2.8 21.2 + - - +
1466r VAL* 3.9 6.3 - - - +
1468r GLU* 1.3 72.4 - - - +
1470r ILE* 1.3 57.2 + - - +
1472r SER* 3.7 5.6 - - - -
1473r ARG* 2.9 30.1 + - - +
1735r HIS* 5.3 13.5 - - + -
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Residues in contact with ILE1470 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1429r PRO* 4.9 11.2 - - + +
1432r TRP* 4.5 20.0 - - + +
1433r ASP* 5.2 5.8 - - + +
1466r VAL 3.0 17.1 + - - +
1467r LEU* 3.1 4.2 + - - +
1469r VAL* 1.3 75.4 - - - +
1471r CYS* 1.3 60.0 + - - +
1473r ARG* 3.8 5.5 - - - +
1474r MET* 2.9 27.7 + - - +
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Residues in contact with CYS1471 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1453r VAL* 5.7 9.0 - - + -
1467r LEU 3.0 13.9 + - - +
1468r GLU* 3.8 7.6 - - - +
1470r ILE* 1.3 74.1 - - - +
1472r SER* 1.3 67.1 + - - +
1474r MET* 3.1 9.7 + - - +
1475r ARG* 3.0 21.1 + - - +
1504r LEU* 6.4 2.7 - - + -
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Residues in contact with SER1472 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1468r GLU 2.9 16.2 + - - -
1469r VAL* 3.7 7.4 - - - -
1471r CYS* 1.3 75.3 - - - +
1473r ARG* 1.3 64.5 + - - +
1475r ARG* 2.8 19.4 + - - +
1476r TYR* 3.0 11.6 + - - +
1757r TRP* 3.5 36.6 - - - +
1758r THR* 4.4 8.1 - - - -
1759r PHE 5.6 0.7 - - - -
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Residues in contact with ARG1473 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1436r SER* 5.4 8.5 - - - +
1469r VAL 2.9 19.5 + - - +
1470r ILE* 3.8 7.0 - - - +
1472r SER* 1.3 74.2 - - - +
1474r MET* 1.3 64.1 + - - +
1476r TYR* 2.9 22.3 + - - +
1477r ILE* 2.9 13.1 + - - +
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Residues in contact with MET1474 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1451r PHE* 5.4 12.8 - - + -
1470r ILE 2.9 15.9 + - - +
1471r CYS* 3.1 14.1 + - - +
1473r ARG* 1.3 74.4 - - - +
1475r ARG* 1.3 63.6 + - - +
1477r ILE* 3.2 8.9 + - - +
1478r SER* 3.0 21.8 + - - -
1485r ILE* 5.5 1.9 - - - +
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Residues in contact with ARG1475 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1471r CYS 3.0 9.1 + - - +
1472r SER* 2.8 17.8 + - - +
1474r MET* 1.3 69.3 - - - +
1476r TYR* 1.3 64.8 + - - +
1478r SER* 3.1 8.2 + - - -
1479r SER* 2.9 21.2 + - - -
1503r TRP 5.5 7.0 - - - +
1504r LEU* 6.3 2.9 - - - -
1757r TRP* 5.8 4.3 - - + +
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Residues in contact with TYR1476 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1472r SER 3.0 9.0 + - - +
1473r ARG* 2.9 18.3 + - - +
1475r ARG* 1.3 72.4 - - - +
1477r ILE* 1.3 63.8 + - - +
1479r SER* 2.9 19.4 + - - -
1480r GLN* 3.0 14.2 + - - +
1757r TRP* 5.8 7.3 - - + +
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Residues in contact with ILE1477 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1439r TRP* 6.0 6.3 - - + -
1445r VAL 6.1 0.2 - - - +
1446r GLN* 5.8 8.7 - - + -
1473r ARG 2.9 10.9 + - - +
1474r MET* 3.4 11.0 - - - +
1476r TYR* 1.3 76.9 - - - +
1478r SER* 1.3 58.9 + - - +
1480r GLN* 2.9 8.4 + - - +
1481r ILE* 2.8 33.3 + - + +
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Residues in contact with SER1478 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1474r MET 3.0 13.3 + - - -
1475r ARG* 3.1 9.6 + - - -
1477r ILE* 1.3 76.6 - - - +
1479r SER* 1.3 61.8 + - - +
1481r ILE* 4.1 2.7 - - - +
1482r GLU* 4.1 5.4 + - - -
1483r ARG 3.5 19.1 - - - +
1484r PRO* 4.9 1.8 - - - +
1485r ILE* 3.9 37.7 - - - +
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Residues in contact with SER1479 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1475r ARG 2.9 12.3 + - - -
1476r TYR* 3.0 17.7 - - - -
1478r SER* 1.3 81.3 - - - +
1480r GLN* 1.3 59.7 + - - +
1481r ILE 3.7 0.2 + - - -
1482r GLU* 3.9 7.1 + - - -
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Residues in contact with GLN1480 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1476r TYR 3.0 9.0 + - - +
1477r ILE* 2.9 7.8 + - - +
1479r SER* 1.3 75.2 - - - +
1481r ILE* 1.3 60.7 + - - +
1482r GLU* 3.1 9.9 + - - +
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Residues in contact with ILE1481 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1446r GLN* 4.8 22.0 - - + +
1477r ILE* 2.8 22.9 + - + +
1478r SER* 4.1 1.3 + - - -
1479r SER 3.5 0.2 - - - -
1480r GLN* 1.3 71.3 - - - +
1482r GLU* 1.3 64.0 + - - +
1483r ARG* 2.8 25.3 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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