Contacts of the helix formed by residues 137 - 145 (chain 7) 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 7).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117 ASP* 4.2 6.4 - - - +
127 ASN 4.1 13.3 + - - +
747 GLY* 5.0 6.3 + - - -
1067 THR* 3.8 23.6 + - - +
1077 GLU* 3.0 35.0 + - - +
1087 ALA* 3.4 11.9 - - - +
1097 PRO* 4.8 7.2 - - + +
1367 ILE* 1.3 73.9 - - - +
1387 ALA* 1.3 59.3 + - - +
1407 LEU* 2.9 23.4 + - - +
1417 SER* 3.1 11.1 + - - -
1547 ASP* 4.0 16.5 - - - +
3397 VAL* 4.0 22.1 - - + +
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Residues in contact with ALA 138 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097 PRO* 5.0 3.1 - - + +
1367 ILE* 3.6 3.3 - - + +
1377 GLN* 1.3 75.0 - - - +
1397 VAL* 1.3 62.8 + - + +
1417 SER* 3.2 3.2 + - - -
1427 LEU* 2.9 21.3 + - - +
1527 VAL* 3.3 33.3 - - + +
1547 ASP* 4.1 8.5 + - + +
1637 VAL* 3.4 44.2 - - + -
1657 ILE* 3.7 2.7 - - + -
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Residues in contact with VAL 139 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1357 ALA* 6.1 1.6 - - + -
1367 ILE* 3.3 38.1 - - + +
1377 GLN 3.0 0.6 + - - -
1387 ALA* 1.3 77.7 - - - +
1407 LEU* 1.3 61.3 + - + +
1427 LEU* 3.5 2.9 + - - +
1437 TYR* 3.3 25.0 + - + +
1657 ILE* 3.5 27.4 - - + -
1687 GLY* 4.2 19.3 - - - +
1707 ALA* 3.9 15.9 - - + +
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Residues in contact with LEU 140 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1047 LEU* 4.4 1.3 - - + -
1067 THR* 3.4 32.5 - - + -
1357 ALA* 3.6 29.8 - - + -
1367 ILE 3.2 7.0 + - - +
1377 GLN 2.9 6.4 + - - +
1397 VAL* 1.3 75.2 - - + +
1417 SER* 1.3 67.6 + - - +
1437 TYR* 3.9 5.8 - - + +
1447 ALA* 3.1 24.6 + - - +
3387 SER 4.3 0.9 - - - -
3397 VAL* 3.3 26.7 - - + +
3427 GLY* 3.4 7.5 - - - +
3437 GLY* 3.8 21.3 - - - +
3467 LEU* 3.7 22.7 - - + -
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Residues in contact with SER 141 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1377 GLN 3.1 7.2 + - - -
1387 ALA* 3.2 11.4 + - - -
1407 LEU* 1.3 77.1 - - - +
1427 LEU* 1.3 51.3 - - - +
1447 ALA* 3.4 0.2 - - - +
1527 VAL* 4.3 5.8 - - - -
2987 VAL* 4.6 1.8 - - - -
3007 SER* 3.0 31.6 + - - -
3387 SER* 3.2 11.9 - - - -
3397 VAL* 3.1 27.7 + - - +
637J LYS* 2.0 44.2 + - - +
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Residues in contact with LEU 142 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1387 ALA 2.9 15.8 + - - +
1397 VAL* 3.8 5.6 - - - +
1407 LEU 3.3 0.2 - - - -
1417 SER* 1.3 75.6 - - - +
1437 TYR* 1.3 59.3 + - + +
1457 SER* 2.9 23.6 + - - -
1477 ARG* 3.4 27.3 + - + +
1487 THR* 3.6 33.4 - - - +
1497 THR 3.8 2.7 - - - +
1507 GLY* 3.8 25.6 - - - +
1527 VAL* 3.8 15.6 - - + +
1657 ILE* 3.9 21.5 - - + -
2987 VAL* 3.7 26.5 - - + -
637J LYS* 3.1 5.6 + - - +
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Residues in contact with TYR 143 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1397 VAL* 3.3 16.8 + - + +
1407 LEU* 3.9 6.1 - - + +
1427 LEU* 1.3 78.2 - - - +
1447 ALA* 1.3 53.5 + - - +
1457 SER 3.0 0.2 - - - -
1477 ARG 3.4 10.3 - - - +
3427 GLY* 3.7 15.5 - - - -
3457 ILE* 3.5 14.4 - - + -
3467 LEU* 3.8 21.8 - - + -
541J MET* 1.9 55.0 - - - +
542J PHE* 2.3 69.0 + + + -
543J PRO* 2.1 47.4 - - + +
637J LYS* 3.7 0.3 - - - +
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Residues in contact with ALA 144 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1407 LEU 3.1 18.8 + - - +
1417 SER 3.4 1.3 - - - +
1437 TYR* 1.3 74.3 - - - +
1457 SER* 1.3 29.1 + - - -
1467 GLY 3.2 2.2 + - - -
3387 SER* 3.5 12.8 - - - +
3427 GLY* 3.5 13.2 - - - +
543J PRO* 4.8 0.2 - - - +
636J LYS* 2.8 10.3 - - - +
637J LYS* 0.7 237.8 + - + +
638J GLY 4.0 0.2 - - - +
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Residues in contact with SER 145 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1427 LEU 2.9 5.2 + - - -
1447 ALA* 1.3 47.0 - - - +
1467 GLY* 1.3 55.4 + - - +
1477 ARG* 3.0 45.2 + - - -
2987 VAL* 3.5 15.1 - - - +
3307 ILE* 5.0 2.5 - - - -
3327 PRO* 4.7 13.5 - - - -
543J PRO* 3.7 0.2 - - - -
544J LYS* 5.2 0.5 - - - +
636J LYS* 5.0 5.2 - - - -
637J LYS* 1.2 91.8 + - - +
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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