Contacts of the helix formed by residues 137 - 145 (chain 5) in PDB entry 1O1F
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 GLN 137 (chain 5).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115 ASP* 4.2 5.9 - - - +
125 ASN 4.1 13.2 + - - +
745 GLY* 5.0 5.5 + - - -
1065 THR* 3.8 22.9 + - - +
1075 GLU* 3.0 34.8 + - - +
1085 ALA* 3.4 11.7 - - - +
1095 PRO* 4.8 6.5 - - + +
1355 ALA 4.6 0.2 - - - -
1365 ILE* 1.3 71.6 - - - +
1385 ALA* 1.3 58.9 + - - +
1405 LEU* 2.9 24.4 + - - +
1415 SER* 3.1 11.1 + - - -
1545 ASP* 4.0 16.8 - - - +
3395 VAL* 4.0 20.4 - - + +
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Residues in contact with ALA 138 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1095 PRO* 5.0 2.9 - - + +
1365 ILE* 3.6 3.7 - - + +
1375 GLN* 1.3 76.0 - - - +
1395 VAL* 1.3 62.8 + - + +
1415 SER* 3.2 3.2 + - - -
1425 LEU* 2.9 21.5 + - - +
1525 VAL* 3.3 34.9 - - + +
1545 ASP* 4.1 8.6 + - + +
1635 VAL* 3.4 43.3 - - + -
1655 ILE* 3.7 2.7 - - + -
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Residues in contact with VAL 139 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1355 ALA* 6.1 0.9 - - + -
1365 ILE* 3.3 38.6 - - + +
1375 GLN 3.0 0.6 + - - -
1385 ALA* 1.3 77.9 - - - +
1405 LEU* 1.3 61.6 + - + +
1425 LEU* 3.5 2.4 + - - +
1435 TYR* 3.3 24.8 + - + +
1655 ILE* 3.5 26.9 - - + -
1685 GLY* 4.2 19.7 - - - +
1705 ALA* 3.9 15.5 - - + -
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Residues in contact with LEU 140 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95 VAL* 6.0 0.2 - - + -
1045 LEU* 4.4 1.3 - - + -
1065 THR* 3.4 33.4 - - + -
1355 ALA* 3.6 28.9 - - + -
1365 ILE 3.2 7.3 + - - +
1375 GLN 2.9 5.9 + - - +
1395 VAL* 1.3 75.0 - - + +
1415 SER* 1.3 66.8 + - - +
1435 TYR* 4.4 6.1 - - + -
1445 ALA* 3.1 25.3 + - - +
3385 SER 3.8 0.8 - - - +
3395 VAL* 3.3 27.1 - - + +
3425 GLY* 3.4 7.5 - - - +
3435 GLY* 3.8 20.6 - - - +
3465 LEU* 3.7 23.6 - - + -
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Residues in contact with SER 141 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1375 GLN 3.1 7.5 + - - -
1385 ALA* 3.2 11.2 + - - -
1405 LEU* 1.3 78.5 - - - +
1425 LEU* 1.3 50.0 - - - +
1525 VAL* 4.3 6.1 - - - -
2985 VAL* 4.6 2.2 - - - -
3005 SER* 3.0 31.7 + - - -
3385 SER* 3.2 10.8 - - - -
3395 VAL* 3.1 27.5 + - - +
637D LYS* 2.0 44.5 + - - +
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Residues in contact with LEU 142 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1385 ALA 2.9 17.4 + - - +
1395 VAL* 3.8 5.6 - - - +
1415 SER* 1.3 75.8 - - - +
1435 TYR* 1.3 59.6 + - - +
1455 SER* 2.9 23.7 + - - -
1475 ARG* 3.4 27.6 + - + +
1485 THR* 3.6 33.2 - - - +
1495 THR 3.8 3.1 - - - +
1505 GLY* 3.8 23.8 - - - +
1525 VAL* 3.8 15.4 - - + +
1655 ILE* 3.9 20.6 - - + -
2985 VAL* 3.7 26.9 - - + -
637D LYS* 3.1 5.8 + - - +
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Residues in contact with TYR 143 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1395 VAL* 3.3 17.2 + - + +
1405 LEU* 3.9 5.6 - - + +
1415 SER 3.3 0.2 - - - -
1425 LEU* 1.3 78.8 - - - +
1445 ALA* 1.3 54.8 + - - +
1455 SER 3.0 0.2 - - - -
1475 ARG 3.4 10.1 - - - +
1485 THR* 6.0 0.4 - - + -
3425 GLY* 3.7 16.2 - - - -
3455 ILE* 3.5 14.1 - - + -
3465 LEU* 3.8 22.4 - - + -
541D MET* 1.9 54.8 - - - +
542D PHE* 2.3 68.0 + + + -
543D PRO* 2.1 47.5 - - + +
637D LYS* 4.3 0.3 - - - -
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Residues in contact with ALA 144 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1405 LEU 3.1 18.2 + - - +
1415 SER 3.4 2.0 - - - +
1435 TYR* 1.3 73.5 - - - +
1455 SER* 1.3 28.3 + - - -
1465 GLY 3.2 2.5 + - - -
3385 SER* 3.5 12.6 - - - +
3425 GLY* 3.5 13.7 - - - +
543D PRO* 4.8 0.2 - - - +
636D LYS* 2.8 11.4 - - - +
637D LYS* 0.7 235.3 + - + +
638D GLY 4.0 0.2 - - - +
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Residues in contact with SER 145 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1425 LEU 2.9 5.1 + - - -
1445 ALA* 1.3 47.5 - - - +
1465 GLY* 1.3 54.4 + - - +
1475 ARG* 3.0 46.1 + - - -
2985 VAL* 3.5 15.2 - - - +
3305 ILE* 5.0 2.7 - - - -
3325 PRO* 4.7 13.0 - - - -
408D VAL* 6.3 0.2 - - - -
543D PRO* 3.7 0.4 - - - -
544D LYS* 5.2 0.7 - - - +
636D LYS* 5.0 5.6 - - - -
637D LYS* 1.2 90.0 + - - +
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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