Contacts of the helix formed by residues 2997 - 3005 (chain H) in PDB entry 2ZLE
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 SER2997 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2948H GLU* 3.1 22.9 - - - -
2964H GLY 3.9 4.2 - - - -
2965H ALA* 4.2 4.9 - - - -
2995H ILE* 3.5 3.8 - - - +
2996H SER* 1.3 83.6 + - - +
2998H PHE* 1.3 68.3 + - - +
2999H ALA* 3.5 9.9 - - - +
3000H ALA* 2.9 31.5 + - - +
3001H LEU* 3.1 10.4 + - - +
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Residues in contact with PHE2998 (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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2944H ILE* 3.0 40.4 - - + -
2945H MET* 4.4 3.1 - - - -
2946H GLY 3.3 35.0 - - - -
2947H THR* 3.7 18.6 - - + +
2948H GLU* 2.5 17.2 + - + +
2965H ALA* 3.7 26.2 - - + +
2966H PHE 4.7 1.1 - - - -
2997H SER* 1.3 68.6 - - - +
2999H ALA* 1.3 54.5 + - - +
3001H LEU* 2.8 11.2 + - + +
3002H ARG* 2.7 69.7 + - + +
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Residues in contact with ALA2999 (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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2948H GLU* 3.6 3.2 + - - +
2997H SER* 3.5 13.2 - - - +
2998H PHE* 1.3 82.2 - - - +
3000H ALA* 1.3 64.8 + - - +
3002H ARG* 3.1 9.3 + - - +
3003H ALA* 3.0 24.2 + - - +
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Residues in contact with ALA3000 (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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2994H PRO 5.4 1.8 - - - +
2995H ILE* 4.8 8.7 - - + -
2996H SER* 4.5 11.7 - - - +
2997H SER* 2.9 28.3 + - - +
2999H ALA* 1.3 75.6 - - - +
3001H LEU* 1.3 56.3 + - - +
3003H ALA* 3.5 5.8 + - - +
3004H GLN* 3.0 37.7 + - + +
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Residues in contact with LEU3001 (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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2942H LEU* 4.4 15.0 - - + -
2944H ILE* 5.4 7.2 - - + -
2965H ALA* 3.8 23.1 - - + -
2987H ILE* 4.2 26.0 - - + -
2990H LEU* 4.5 9.6 - - + -
2995H ILE* 3.8 25.5 - - + +
2997H SER 3.1 1.7 + - - +
2998H PHE* 2.8 22.8 + - + +
3000H ALA* 1.3 71.3 - - - +
3002H ARG* 1.3 66.2 + - - +
3003H ALA 3.1 1.6 - - - -
3004H GLN* 3.1 5.6 + - - +
3005H VAL* 2.9 52.6 + - + +
3016H LEU* 5.1 0.7 - - + -
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Residues in contact with ARG3002 (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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2818H ARG* 2.6 78.4 + - - +
2998H PHE* 2.7 53.3 + - + +
2999H ALA* 3.7 8.1 - - - +
3001H LEU* 1.3 72.8 - - - +
3003H ALA* 1.3 59.5 + - - +
3005H VAL* 3.0 18.3 - - + +
3006H GLY 3.5 3.1 + - - -
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Residues in contact with ALA3003 (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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2818H ARG* 5.0 4.5 - - - +
2873H GLU* 4.3 21.3 - - - +
2999H ALA 3.0 15.6 + - - +
3000H ALA* 3.7 6.1 - - - +
3002H ARG* 1.3 76.9 - - - +
3004H GLN* 1.3 63.5 + - + +
3006H GLY* 3.2 13.7 + - - -
3007H THR* 3.6 11.3 + - - -
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Residues in contact with GLN3004 (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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2990H LEU* 3.0 43.1 + - + +
2993H LYS* 4.7 18.6 + - - +
2994H PRO 4.3 5.9 - - - +
2995H ILE* 3.6 18.6 - - - +
3000H ALA* 3.0 22.9 + - - +
3001H LEU* 3.1 5.6 + - - +
3003H ALA* 1.3 71.4 - - + +
3005H VAL* 1.3 62.3 + - - +
3006H GLY 3.0 5.2 - - - -
3007H THR* 3.1 14.3 + - - -
3008H MET* 2.9 30.6 - - + +
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Residues in contact with VAL3005 (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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2818H ARG* 4.4 5.4 - - - +
2939H ARG* 5.9 0.2 - - - +
2940H GLY 3.5 22.6 - - - +
2941H GLU* 5.9 0.7 - - - -
2942H LEU* 4.3 23.8 - - + +
2990H LEU* 4.3 2.9 - - + -
3001H LEU* 2.9 40.0 + - + +
3002H ARG* 3.0 24.0 - - + +
3004H GLN* 1.3 75.8 - - - +
3006H GLY* 1.3 58.0 + - - +
3007H THR 3.2 1.9 + - - -
3008H MET* 3.7 21.8 + - - +
3014H LEU* 4.0 22.7 - - + -
3029H LEU* 4.7 2.9 - - + +
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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