Contacts of the helix formed by residues 1554 - 1572 (chain A) in PDB entry 5M64
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 GLY1554 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1549A VAL 3.5 0.6 + - - -
1550A LEU* 3.2 21.2 + - - +
1553A TYR* 1.3 79.8 - - - +
1555A VAL* 1.3 60.7 + - - -
1556A GLU* 3.5 2.9 - - - -
1557A ALA* 3.5 3.0 + - - -
1558A ALA 3.0 22.7 + - - -
182E ASP* 3.3 26.7 - - - -
183E PRO* 4.9 0.4 - - - +
184E VAL* 4.2 2.0 - - - -
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Residues in contact with VAL1555 (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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1550A LEU* 4.1 10.8 - - + -
1554A GLY* 1.3 72.0 - - - -
1556A GLU* 1.3 67.3 + - + +
1558A ALA* 3.1 7.7 + - - +
1559A ARG* 3.0 21.8 + - - +
1590A THR* 3.6 34.5 - - + +
1593A GLY* 3.3 27.6 - - - +
177E ARG 5.5 0.4 - - - +
178E ILE* 3.6 35.2 - - + -
179E GLN 5.8 0.2 - - - +
182E ASP* 3.8 6.3 + - - +
212E ARG* 3.9 21.1 - - - +
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Residues in contact with GLU1556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1554A GLY* 5.4 0.4 - - - -
1555A VAL* 1.3 83.1 - - + +
1557A ALA* 1.3 63.2 + - - +
1559A ARG* 3.1 12.5 + - + +
1560A ASN* 3.0 33.6 + - - +
150E VAL* 6.2 0.7 - - + -
151E PRO* 3.3 26.3 - - + +
153E HIS* 2.3 44.3 + - + +
178E ILE* 6.1 1.1 - - + -
198E ILE* 3.3 30.8 - - - +
200E ARG* 3.6 14.8 + - - +
212E ARG* 4.6 20.7 - - - +
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Residues in contact with ALA1557 (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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1549A VAL* 4.2 2.2 - - - +
1553A TYR* 3.6 37.5 - - + +
1554A GLY 3.5 4.4 + - - +
1555A VAL 3.3 0.4 - - - -
1556A GLU* 1.3 84.4 - - + +
1558A ALA* 1.3 59.9 + - - +
1560A ASN 3.5 0.9 + - - -
1561A THR* 3.4 20.4 + - - +
149E LEU* 3.4 27.9 - - + +
150E VAL* 3.6 19.5 - - + -
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Residues in contact with ALA1558 (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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1546A VAL* 4.9 2.0 - - + +
1549A VAL* 3.6 23.1 + - + +
1550A LEU* 3.7 16.4 - - + -
1554A GLY 3.0 14.0 + - - +
1555A VAL* 3.1 10.1 + - - +
1557A ALA* 1.3 75.2 - - - +
1559A ARG* 1.3 59.4 + - - +
1561A THR* 3.2 10.7 - - - +
1562A ILE* 3.0 36.6 + - + +
1590A THR* 5.5 5.8 - - + -
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Residues in contact with ARG1559 (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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1047A GLN* 4.9 8.5 - - - +
1555A VAL* 3.0 13.3 + - + +
1556A GLU* 3.1 14.0 + - + +
1558A ALA* 1.3 76.6 - - - +
1560A ASN* 1.3 80.7 + - - +
1562A ILE* 3.4 7.7 - - + +
1563A VAL* 3.0 39.3 + - - +
1583A ASP* 3.5 25.5 + - - -
1586A ALA* 3.6 38.4 - - + +
1587A ASP* 4.3 8.7 - - + +
1590A THR* 5.4 8.3 + - - +
200E ARG* 3.1 32.3 - - - +
201E LYS 5.6 0.6 + - - -
208E TYR* 2.9 28.2 + - - -
212E ARG* 5.8 4.7 - - - +
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Residues in contact with ASN1560 (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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1556A GLU 3.0 17.0 + - - +
1557A ALA 4.0 0.4 - - - +
1558A ALA 3.3 0.4 - - - -
1559A ARG* 1.3 107.1 + - - +
1561A THR* 1.3 51.3 + - - +
1563A VAL* 3.3 10.3 - - - +
1564A ASN* 2.7 35.5 + - - -
148E GLU 5.2 1.2 + - - -
149E LEU* 3.0 39.9 + - + +
151E PRO* 3.8 19.0 - - - +
200E ARG* 5.2 3.7 - - - +
201E LYS 5.4 3.5 - - - +
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Residues in contact with THR1561 (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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1542A THR* 5.2 5.9 - - - +
1543A SER 3.7 23.6 + - - +
1545A ASP 5.3 0.9 - - - +
1549A VAL* 3.8 25.6 - - + +
1557A ALA 3.4 14.2 + - - +
1558A ALA* 3.2 21.3 - - - +
1560A ASN* 1.3 78.7 - - - +
1562A ILE* 1.3 61.7 + - + +
1563A VAL 3.4 0.9 - - - -
1564A ASN* 3.5 8.7 + - - +
1565A GLU* 3.1 22.7 + - - +
149E LEU* 3.9 13.7 - - - -
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Residues in contact with ILE1562 (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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1225A ILE* 5.5 6.3 - - + -
1544A ASN 5.7 1.1 - - - +
1545A ASP 5.5 0.2 - - - +
1546A VAL* 3.6 35.9 - - + -
1549A VAL* 5.0 0.4 - - + -
1558A ALA* 3.0 25.7 + - + +
1559A ARG* 3.4 9.6 - - + +
1561A THR* 1.3 78.7 - - + +
1563A VAL* 1.3 65.9 + - - +
1564A ASN 3.1 1.6 - - - -
1565A GLU* 3.0 25.0 + - + +
1566A ILE* 3.1 23.1 + - + +
1585A ILE* 6.3 0.4 - - + -
1586A ALA* 3.7 34.8 - - + +
1589A MET* 5.5 9.4 - - + -
1590A THR* 5.2 6.1 - - - +
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Residues in contact with VAL1563 (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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1559A ARG* 3.0 28.3 + - - +
1560A ASN* 3.3 19.1 - - - +
1562A ILE* 1.3 79.1 - - - +
1564A ASN* 1.3 68.0 + - - +
1566A ILE* 3.3 12.7 - - - +
1567A ASN* 3.0 23.1 - - - +
1579A PHE* 4.9 6.5 - - + +
1582A LEU* 4.2 23.6 - - + +
1583A ASP* 3.4 26.0 - - - +
1586A ALA* 4.7 6.5 - - + -
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Residues in contact with ASN1564 (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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1560A ASN 2.7 21.8 + - - +
1561A THR* 3.5 10.3 + - - +
1562A ILE 3.1 0.2 - - - -
1563A VAL* 1.3 84.8 - - - +
1565A GLU* 1.3 59.6 + - - +
1567A ASN* 3.7 10.9 - - - +
1568A ASN* 3.0 27.7 + - - +
149E LEU* 4.8 6.9 - - - +
203E GLU* 5.7 1.4 - - - +
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Residues in contact with GLU1565 (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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1221A ARG* 2.6 43.9 + - - +
1222A LEU* 5.9 0.2 - - - -
1225A ILE* 3.8 19.1 - - - +
1544A ASN* 3.4 30.1 - - - +
1546A VAL* 6.3 0.7 - - + -
1561A THR 3.1 13.6 + - - +
1562A ILE* 3.0 16.5 + - + +
1564A ASN* 1.3 74.5 - - - +
1566A ILE* 1.3 83.7 + - - +
1568A ASN* 3.2 5.8 + - - +
1569A VAL* 3.0 36.8 + - + +
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Residues in contact with ILE1566 (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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1222A LEU* 3.7 28.9 - - + -
1225A ILE* 5.1 9.0 - - + -
1226A VAL* 5.1 4.5 - - + -
1562A ILE* 3.1 16.8 - - + +
1563A VAL* 3.3 27.4 - - + +
1565A GLU* 1.3 91.5 + - - +
1567A ASN* 1.3 67.2 + - + +
1569A VAL* 4.2 5.6 - - + -
1570A PHE* 3.0 41.9 + - + -
1582A LEU* 3.6 41.3 - - + +
1585A ILE* 6.5 0.7 - - + -
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Residues in contact with ASN1567 (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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1563A VAL* 3.0 24.6 + - - +
1564A ASN* 3.7 13.5 - - - +
1565A GLU 3.1 0.6 - - - -
1566A ILE* 1.3 81.8 - - + +
1568A ASN* 1.3 56.9 + - - +
1570A PHE* 3.5 6.2 + - - +
1571A SER* 2.8 34.1 + - - +
1577A VAL* 5.6 4.6 - - - +
1579A PHE* 3.1 43.2 - - - -
1582A LEU* 6.0 1.8 - - + -
203E GLU* 5.3 0.5 - - - +
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Residues in contact with ASN1568 (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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1564A ASN 3.0 19.1 + - - +
1565A GLU* 3.6 5.4 - - - +
1567A ASN* 1.3 75.2 - - - +
1569A VAL* 1.3 67.7 + - + +
1571A SER* 3.1 7.8 + - - -
1572A ARG* 2.9 40.2 + - - +
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Residues in contact with VAL1569 (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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1200A MET* 5.7 3.1 - - - +
1216A THR 5.4 1.8 - - - +
1217A LEU* 5.2 5.2 - - + -
1218A GLY* 4.2 31.6 - - - +
1221A ARG* 3.8 17.5 - - + +
1222A LEU* 5.0 9.6 - - + +
1565A GLU* 3.0 41.2 + - + +
1566A ILE* 4.0 8.3 - - + +
1568A ASN* 1.3 77.0 - - + +
1570A PHE* 1.3 71.6 + - + +
1572A ARG* 3.4 19.4 + - - +
1573A TYR* 4.3 12.0 + - + -
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Residues in contact with PHE1570 (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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1192A SER 5.4 2.2 - - - -
1193A VAL* 3.7 28.5 - - + -
1196A PRO* 5.5 6.7 - - + -
1200A MET* 3.6 35.4 - - + -
1222A LEU* 4.1 20.6 - - + -
1566A ILE* 3.0 25.7 + - + +
1567A ASN* 3.9 6.7 - - - +
1569A VAL* 1.3 82.5 - - + +
1571A SER* 1.3 62.8 + - - +
1572A ARG 3.1 1.5 + - - -
1573A TYR* 3.3 7.9 + - - +
1575A ILE* 3.1 44.4 + - + +
1577A VAL* 3.9 26.7 - - + -
1582A LEU* 3.9 27.1 - - + -
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Residues in contact with SER1571 (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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1567A ASN* 2.8 28.7 + - - +
1568A ASN* 3.1 11.6 + - - -
1570A PHE* 1.3 72.2 - - - +
1572A ARG* 1.3 64.4 + - - +
1573A TYR 3.2 0.6 + - - -
1574A ALA* 3.5 11.0 + - - +
1575A ILE 4.4 7.9 - - - -
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Residues in contact with ARG1572 (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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1205A PHE* 4.2 23.6 + - - -
1217A LEU* 3.6 35.4 - - + +
1568A ASN* 2.9 40.0 + - - +
1569A VAL* 3.6 12.3 - - - +
1570A PHE 3.1 1.0 - - - -
1571A SER* 1.3 79.7 - - - +
1573A TYR* 1.3 70.6 + - + +
1574A ALA* 3.4 1.5 + - - +
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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