Contacts of the helix formed by residues 2618 - 2629 (chain H) in PDB entry 6X34
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 SER2618 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2616H ARG* 3.1 1.4 - - - +
2617H PRO* 1.3 82.4 - - - +
2619H MET* 1.3 63.8 + - - +
2620H LEU 3.6 0.2 - - - -
2621H GLN* 4.2 1.3 - - - -
2622H HIS* 3.4 24.3 + - - +
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Residues in contact with MET2619 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2616H ARG* 3.7 18.2 + - + +
2618H SER* 1.3 80.0 - - - +
2620H LEU* 1.3 62.1 + - - +
2622H HIS* 4.3 1.1 - - - +
2623H LEU* 3.2 26.7 + - - +
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Residues in contact with LEU2620 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2584H LEU* 6.2 4.5 - - + -
2615H ILE* 3.7 32.1 - - + -
2616H ARG 3.4 8.4 + - - +
2619H MET* 1.3 78.4 - - - +
2621H GLN* 1.3 61.8 + - - +
2623H LEU* 4.2 3.5 - - - +
2624H LEU* 3.0 32.6 + - - +
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Residues in contact with GLN2621 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2616H ARG 4.3 1.0 + - - -
2617H PRO* 3.2 26.7 + - + +
2618H SER* 4.1 1.5 + - - +
2619H MET 3.5 0.2 - - - -
2620H LEU* 1.3 78.8 - - - +
2622H HIS* 1.3 60.6 + - - +
2624H LEU* 4.6 2.3 - - - +
2625H ARG* 3.3 25.3 + - - +
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Residues in contact with HIS2622 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2618H SER 3.4 18.0 + - - +
2619H MET 4.3 1.6 - - - +
2620H LEU 3.3 0.4 - - - -
2621H GLN* 1.3 79.9 - - - +
2623H LEU* 1.3 63.4 + - - +
2625H ARG* 4.0 2.3 - - - +
2626H ARG* 3.2 25.1 + - - +
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Residues in contact with LEU2623 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2581H ASP* 3.8 44.9 - - + +
2584H LEU* 6.0 1.8 - - + -
2585H HIS* 6.3 1.1 - - + -
2619H MET 3.2 20.0 + - - +
2620H LEU* 4.2 3.8 - - - +
2622H HIS* 1.3 76.5 - - - +
2624H LEU* 1.3 68.3 + - - +
2626H ARG* 3.5 7.8 + - - +
2627H LEU* 3.4 38.8 - - + +
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Residues in contact with LEU2624 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2584H LEU* 5.3 16.4 - - + +
2620H LEU* 3.0 19.8 + - + +
2621H GLN* 4.6 2.5 - - - +
2623H LEU* 1.3 80.8 - - + +
2625H ARG* 1.3 63.0 + - - +
2626H ARG 3.5 0.2 + - - -
2627H LEU* 3.7 4.1 + - - +
2628H VAL* 3.5 20.7 + - - +
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Residues in contact with ARG2625 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2621H GLN 3.3 20.2 + - - +
2622H HIS* 4.3 3.4 - - - +
2623H LEU 3.4 0.6 - - - -
2624H LEU* 1.3 75.9 - - - +
2626H ARG* 1.3 63.4 + - - +
2628H VAL* 3.7 8.5 - - + -
2629H PHE* 3.2 47.3 + - + -
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Residues in contact with ARG2626 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2622H HIS 3.2 20.0 + - - +
2623H LEU* 3.8 7.4 - - - +
2624H LEU 3.3 0.6 - - - -
2625H ARG* 1.3 77.4 - - - +
2627H LEU* 1.3 68.5 + - + +
2629H PHE* 3.5 16.9 + - - +
2906H VAL* 5.6 4.7 - - - +
2910H THR* 5.0 20.8 - - - +
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Residues in contact with LEU2627 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2585H HIS* 3.8 29.2 - - + -
2623H LEU* 3.4 31.5 + - + +
2624H LEU* 3.7 4.5 + - - +
2625H ARG 3.4 0.2 - - - -
2626H ARG* 1.3 85.4 - - + +
2628H VAL* 1.3 62.1 + - - +
2629H PHE 3.5 2.8 + - - -
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Residues in contact with VAL2628 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2588H TYR* 3.5 48.2 - - + +
2624H LEU 3.5 13.7 + - - +
2625H ARG* 3.4 18.6 - - - +
2627H LEU* 1.3 78.3 - - - +
2629H PHE* 1.3 87.1 + - + +
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Residues in contact with PHE2629 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2625H ARG* 3.2 34.5 + - + +
2626H ARG* 3.5 12.3 + - - +
2627H LEU 3.3 3.4 - - - +
2628H VAL* 1.3 100.5 - - + +
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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