Contacts of the strand formed by residues 2861 - 2870 (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 THR2861 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2851H ALA 3.9 0.5 - - - +
2852H ILE* 3.5 1.7 - - - -
2853H GLY 2.8 30.5 + - - -
2855H PRO* 2.9 36.3 - - + +
2859H GLY 4.1 4.2 + - - -
2860H GLU* 1.3 72.0 - - - +
2862H VAL* 1.3 63.0 + - - +
2863H THR* 4.2 3.4 + - - +
2882H ILE* 5.8 1.3 - - + -
3264I SER* 3.5 33.0 - - - +
3265I ALA* 4.9 1.4 - - - +
3273I GLN* 3.8 17.3 + - - +
3311I ILE* 3.7 18.2 - - + -
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Residues in contact with VAL2862 (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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2731H LEU* 3.8 18.8 - - + -
2735H MET* 5.2 8.3 - - + -
2850H VAL* 3.7 20.6 - - + -
2851H ALA 3.2 8.1 - - - +
2852H ILE* 4.3 13.9 - - + -
2860H GLU 4.8 3.6 - - - +
2861H THR* 1.3 76.0 - - - +
2863H THR* 1.3 60.6 + - - +
3241I VAL* 3.1 30.5 - - + -
3262I ILE* 3.6 21.7 - - + +
3264I SER* 2.7 35.3 + - - +
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Residues in contact with THR2863 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2850H VAL* 3.5 3.1 - - - +
2851H ALA* 2.8 51.4 + - + +
2861H THR* 5.6 3.4 - - - +
2862H VAL* 1.3 76.6 - - - +
2864H SER* 1.3 59.8 + - - +
2880H ALA* 3.8 11.4 - - - +
2881H ALA 3.3 26.8 + - - +
2882H ILE* 5.2 8.3 - - + +
3262I ILE* 4.0 3.4 - - - -
3264I SER* 4.7 1.1 - - - -
3275I ASP* 2.7 32.9 + - - +
3311I ILE* 6.1 0.7 - - - -
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Residues in contact with SER2864 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2727H LEU* 4.0 26.9 - - - +
2849H THR 3.5 10.1 - - - -
2850H VAL* 4.3 2.0 - - - +
2863H THR* 1.3 74.9 + - - +
2865H GLY* 1.3 60.8 + - - +
2879H ASP* 4.7 1.9 - - - +
2880H ALA* 3.6 14.3 - - - +
3244I TYR* 5.2 3.5 - - - -
3261I GLY* 5.6 2.6 - - - -
3262I ILE* 3.9 16.2 - - - +
3275I ASP* 3.3 14.6 + - - +
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Residues in contact with GLY2865 (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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2848H TYR* 3.4 10.4 - - - -
2849H THR* 2.8 31.6 + - - +
2864H SER* 1.3 79.9 + - - +
2866H ILE* 1.3 70.2 + - - +
2879H ASP* 3.4 12.8 - - - -
2880H ALA* 3.9 3.1 - - - +
3656J SER* 5.6 3.1 - - - -
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Residues in contact with ILE2866 (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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2845H VAL 4.2 11.0 - - - +
2846H GLY* 4.0 7.0 - - - +
2847H ASP 3.1 10.5 - - - +
2848H TYR* 3.4 28.7 - - + -
2849H THR* 3.8 6.1 - - - +
2865H GLY* 1.3 80.5 - - - +
2867H VAL* 1.3 61.5 + - - +
2868H SER 3.3 2.4 + - - -
2878H THR* 2.6 29.1 + - - -
2879H ASP* 3.0 18.6 + - - +
3519J LEU* 4.2 12.1 - - + -
3654J VAL* 3.6 40.8 - - + +
3656J SER* 3.9 24.0 - - - +
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Residues in contact with VAL2867 (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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2843H LEU* 4.6 19.1 - - + -
2844H ARG 3.4 21.3 - - - +
2845H VAL* 2.3 48.9 - - + +
2847H ASP* 2.7 23.5 + - + +
2848H TYR 5.1 0.2 - - - +
2849H THR* 3.8 14.8 - - - +
2866H ILE* 1.3 71.9 - - - +
2868H SER* 1.3 58.9 + - - +
2869H ALA 4.4 1.8 - - - +
2870H LEU* 3.8 28.7 - - + -
2876H ILE* 4.6 6.7 - - + -
2877H GLN 3.8 6.7 - - - +
2878H THR* 4.5 2.5 - - - -
2899H ILE* 5.0 1.8 - - + -
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Residues in contact with SER2868 (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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2845H VAL* 3.8 3.9 - - - +
2866H ILE 3.3 3.5 + - - -
2867H VAL* 1.3 74.7 - - - +
2869H ALA* 1.3 58.1 + - - +
2877H GLN* 2.6 19.9 + - - -
2879H ASP* 3.6 22.2 + - - +
2915H ILE* 3.6 15.3 - - - +
3652J GLU 3.9 2.3 - - - +
3653J THR* 3.5 20.5 - - - +
3654J VAL* 2.7 50.0 + - - +
3655J THR* 4.5 0.7 - - - -
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Residues in contact with ALA2869 (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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2845H VAL* 4.4 5.4 - - - -
2867H VAL* 3.6 1.0 + - - -
2868H SER* 1.3 79.4 - - - +
2870H LEU* 1.3 65.9 + - - +
2871H GLY* 3.4 5.9 + - - +
2877H GLN* 2.9 64.3 + - + +
3652J GLU 4.7 11.0 - - - +
3653J THR* 4.7 2.2 - - + +
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Residues in contact with LEU2870 (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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2843H LEU* 3.0 49.1 - - + +
2844H ARG* 3.5 17.0 - - - +
2845H VAL* 4.0 10.5 - - + +
2867H VAL* 3.8 15.0 - - + -
2869H ALA* 1.3 77.7 - - - +
2871H GLY* 1.3 50.6 + - - +
2872H ARG* 2.4 53.7 + - - +
2874H ASN* 3.2 20.3 - - - +
2875H PHE 4.5 0.2 - - - -
2876H ILE* 4.1 25.1 - - + -
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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