Contacts of the helix formed by residues 1258 - 1275 (chain 1) in PDB entry 6AH0
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 ALA1258 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12561 HIS 2.9 12.6 + - - +
12571 PRO* 1.3 80.8 - - - +
12591 ARG* 1.3 67.4 + - - +
12601 LYS 3.5 1.6 - - - +
12611 VAL* 4.6 3.1 - - - +
12621 ARG* 3.9 6.9 + - - -
56H A 3.2 29.3 + - - -
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Residues in contact with ARG1259 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12571 PRO 3.7 0.4 + - - -
12581 ALA* 1.3 72.3 - - - +
12601 LYS* 1.3 67.3 + - - +
12621 ARG* 2.9 14.9 + - - -
12631 ASP* 2.9 11.6 + - - -
56H A 2.6 24.1 + - - -
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Residues in contact with LYS1260 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12581 ALA* 3.5 1.4 - - - +
12591 ARG* 1.3 74.7 - - - +
12611 VAL* 1.3 64.1 + - - +
12631 ASP* 3.2 8.6 + - - +
12641 VAL* 3.5 7.1 + - - -
56H A 4.4 1.6 + - - -
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Residues in contact with VAL1261 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12531 GLY* 4.7 5.4 - - - -
12581 ALA* 4.5 3.6 + - - +
12591 ARG 3.2 0.8 - - - -
12601 LYS* 1.3 75.5 - - - +
12621 ARG* 1.3 56.3 + - - +
12641 VAL* 2.8 19.6 + - - +
12651 TYR* 2.9 14.4 + - - -
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Residues in contact with ARG1262 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12531 GLY 4.2 15.0 + - - -
12541 LEU 4.2 11.5 - - - +
12561 HIS* 4.8 4.2 + - - +
12581 ALA 3.9 9.2 + - - -
12591 ARG 2.9 11.2 + - - -
12611 VAL* 1.3 67.4 - - - +
12631 ASP* 1.3 68.8 + - - +
12651 TYR 4.7 0.4 - - - +
12661 TRP* 3.0 19.2 + - - +
247 ALA* 4.3 18.6 + - - +
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Residues in contact with ASP1263 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12591 ARG 2.9 12.7 + - - -
12601 LYS* 3.7 5.2 - - - +
12611 VAL 3.1 0.4 + - - -
12621 ARG* 1.3 79.3 - - - +
12641 VAL* 1.3 56.1 + - - +
12661 TRP* 3.8 0.7 - - - -
12671 LYS* 3.1 18.0 + - - -
247 ALA* 5.0 6.1 + - - +
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Residues in contact with VAL1264 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12601 LYS 3.5 6.1 + - - -
12611 VAL* 2.8 12.6 + - - +
12631 ASP* 1.3 68.9 - - - +
12651 TYR* 1.3 58.1 + - - +
12661 TRP 2.9 1.1 - - - -
12671 LYS* 2.3 29.8 + - - +
12681 ILE* 2.8 9.9 + - - -
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Residues in contact with TYR1265 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12501 CYS* 5.3 10.1 - - - +
12531 GLY* 5.2 14.4 - - - -
12541 LEU* 5.6 5.6 - - - -
12611 VAL 2.9 15.5 + - - -
12621 ARG 5.0 0.2 - - - -
12641 VAL* 1.3 69.4 - - - +
12661 TRP* 1.3 56.9 + - - +
12681 ILE* 3.9 2.6 - - - +
12691 TYR* 2.9 25.5 + - - -
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Residues in contact with TRP1266 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12541 LEU* 5.5 4.3 - - - +
12621 ARG* 3.0 17.7 + - - +
12631 ASP 3.8 0.9 - - - -
12641 VAL 2.7 4.2 + - - -
12651 TYR* 1.3 72.9 - - - +
12671 LYS* 1.3 65.9 + - - +
12691 TYR* 3.1 1.4 + - - +
12701 ASN* 2.9 22.0 + - - -
227 GLY 5.7 5.2 - - - +
237 HIS* 5.8 9.4 - - - +
247 ALA* 6.1 0.2 - - - +
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Residues in contact with LYS1267 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12631 ASP 3.1 11.2 + - - -
12641 VAL* 2.3 18.0 + - - +
12661 TRP* 1.3 69.2 - - - +
12681 ILE* 1.3 64.5 + - - +
12701 ASN* 3.4 1.8 + - - +
12711 SER* 3.1 13.2 + - - -
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Residues in contact with ILE1268 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12641 VAL 2.8 10.1 + - - -
12651 TYR* 3.9 3.4 - - - +
12671 LYS* 1.3 73.5 - - - +
12691 TYR* 1.3 54.3 + - - +
12711 SER* 2.4 28.5 + - - +
12721 ILE 2.9 9.9 + - - -
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Residues in contact with TYR1269 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12501 CYS* 6.4 1.3 - - - +
12651 TYR 2.9 20.3 + - - -
12661 TRP* 3.7 0.9 - - - +
12681 ILE* 1.3 70.4 - - - +
12701 ASN* 1.3 60.1 + - - +
12721 ILE* 3.6 3.6 + - - +
12731 TYR* 2.9 19.1 + - - -
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Residues in contact with ASN1270 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12661 TRP 2.9 14.9 + - - -
12671 LYS* 3.7 4.0 - - - +
12681 ILE 2.8 0.6 + - - -
12691 TYR* 1.3 74.7 - - - +
12711 SER* 1.3 53.8 + - - +
12731 TYR* 2.2 28.0 + - - +
12741 ILE* 2.9 10.9 + - - -
217 THR* 6.1 2.7 - - - +
227 GLY 5.8 5.6 - - - +
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Residues in contact with SER1271 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12351 GLU* 6.5 0.9 - - - -
12671 LYS 3.1 9.1 + - - -
12681 ILE* 2.4 15.0 + - - +
12701 ASN* 1.3 70.4 - - - +
12721 ILE* 1.3 61.3 + - - +
12741 ILE* 3.7 5.6 + - - +
12751 GLY* 4.2 5.4 + - - -
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Residues in contact with ILE1272 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12681 ILE 2.9 10.5 + - - -
12691 TYR* 3.7 4.9 - - - +
12711 SER* 1.3 76.9 - - - +
12731 TYR* 1.3 58.3 + - - +
12751 GLY* 2.7 20.6 - - - +
12761 SER 4.8 1.4 - - - -
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Residues in contact with TYR1273 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12691 TYR 2.9 12.2 + - - -
12701 ASN* 2.2 22.9 + - - +
12721 ILE* 1.3 72.2 - - - +
12741 ILE* 1.3 63.2 + - - +
12751 GLY 2.9 5.7 - - - +
12761 SER 5.7 0.2 - - - -
12771 GLN* 3.6 14.9 + - - +
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Residues in contact with ILE1274 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12701 ASN 2.9 9.5 + - - -
12711 SER 3.7 1.4 + - - -
12721 ILE 3.4 0.4 - - - -
12731 TYR* 1.3 79.0 - - - +
12751 GLY* 1.3 61.9 + - - +
12761 SER 3.6 1.2 + - - -
12771 GLN* 3.7 5.0 + - - -
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Residues in contact with GLY1275 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12711 SER 4.2 5.8 + - - -
12721 ILE 2.7 24.2 + - - +
12731 TYR 2.9 2.4 - - - +
12741 ILE* 1.3 74.4 - - - +
12761 SER* 1.3 56.6 + - - -
12771 GLN 2.7 8.3 + - - -
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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
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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