Contacts of the strand formed by residues 899 - 907 (chain D) in PDB entry 3N1Q
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 SER 899 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A ASN* 3.3 23.8 - - - +
868D PRO* 3.6 1.2 - - - +
869D THR* 2.7 42.6 + - - +
898D THR* 1.3 85.0 - - - +
900D TYR* 1.3 70.5 + - - +
920D ILE* 3.3 18.9 - - - +
921D CYS 3.5 5.7 + - - -
922D GLU* 4.1 12.2 + - - +
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Residues in contact with TYR 900 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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843D ILE* 4.1 12.6 - - + -
866D TYR* 4.7 8.7 - + + -
867D ARG 3.3 25.1 - - - +
868D PRO* 4.0 21.1 - - + +
869D THR* 3.3 5.8 - - - -
894D LEU* 3.6 45.2 - - + +
895D GLN* 3.1 29.6 + - - +
898D THR* 3.7 31.3 - - + +
899D SER* 1.3 85.0 + - - +
901D ASP* 1.3 60.0 + - - +
902D ILE* 3.7 10.8 + - + +
919D MET 3.5 1.2 - - - +
920D ILE* 3.2 6.6 - - - -
921D CYS 2.8 34.6 + - - +
923D THR* 4.1 2.9 - - + -
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Residues in contact with ASP 901 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A LYS* 2.8 32.6 + - - -
90A GLU* 4.7 2.0 - - + -
865D TYR 3.5 1.0 - - - +
866D TYR* 3.2 7.3 - - - -
867D ARG* 2.7 50.9 + - - +
869D THR* 2.9 30.7 + - - +
877D TYR* 3.6 22.9 - - + +
900D TYR* 1.3 72.3 - - - +
902D ILE* 1.3 60.4 + - - +
903D LYS 4.1 0.4 - - - -
918D VAL* 4.2 8.7 - - + -
919D MET 3.4 5.4 - - - -
920D ILE* 4.1 7.1 - - - +
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Residues in contact with ILE 902 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832D ILE* 3.6 11.2 - - + +
835D THR* 4.2 10.8 - - + -
843D ILE* 3.6 35.7 - - + -
845D LEU* 3.9 29.8 - - + -
864D ILE* 4.5 3.1 - - + -
865D TYR 3.5 8.1 - - - +
866D TYR* 4.7 2.5 - - + -
891D ILE* 4.1 19.1 - - + -
900D TYR* 3.9 13.9 - - + +
901D ASP* 1.3 77.4 - - - +
903D LYS* 1.3 62.3 + - - +
918D VAL* 3.6 1.2 - - - +
919D MET* 2.7 40.7 + - + +
921D CYS* 3.9 17.7 - - + +
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Residues in contact with LYS 903 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A GLU 4.6 8.3 + - - +
92A ASN* 4.6 5.7 - - - +
832D ILE* 4.3 2.0 - - - -
864D ILE* 3.9 0.5 - - - +
865D TYR* 2.7 43.9 + - + +
874D ASP* 4.4 14.3 + - - +
877D TYR* 3.5 47.9 + - + +
902D ILE* 1.3 76.5 - - - +
904D MET* 1.3 57.1 + - - +
915D PHE* 3.7 50.4 - - + +
916D SER* 4.0 9.2 - - - +
917D ASN 4.3 4.0 - - - -
918D VAL* 3.7 29.2 - - + -
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Residues in contact with MET 904 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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830D PRO* 4.3 6.7 - - + -
832D ILE* 4.0 12.1 - - + -
845D LEU* 4.4 4.9 - - + -
847D TRP* 3.4 60.6 - - + -
862D PHE* 3.6 22.4 - - + -
863D TYR 3.1 13.2 - - - +
864D ILE* 3.6 28.0 - - + -
865D TYR* 4.5 0.7 - - - -
903D LYS* 1.3 75.8 - - - +
905D GLN* 1.3 67.2 + - - +
915D PHE* 3.4 5.8 - - - -
916D SER* 2.8 44.7 + - - +
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Residues in contact with GLN 905 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830D PRO* 3.7 12.1 - - - -
862D PHE* 3.4 2.4 - - - -
863D TYR* 2.7 39.7 + - + +
865D TYR* 2.9 32.7 + - + -
904D MET* 1.3 83.9 - - - +
906D CYS* 1.3 59.7 + - - +
912D GLU* 3.6 24.1 - - + +
913D SER* 2.7 33.3 + - - +
914D GLU 4.1 3.8 - - - +
915D PHE* 3.8 29.7 - - - +
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Residues in contact with CYS 906 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829D GLY* 5.1 0.4 - - - -
830D PRO* 3.5 10.1 - - + +
849D TYR* 3.4 35.9 - - + -
859D ILE* 4.4 10.8 - - + -
861D GLY 3.4 7.6 - - - +
862D PHE* 3.4 28.3 - - + -
905D GLN* 1.3 75.1 - - - +
907D PHE* 1.3 61.2 + - - +
912D GLU* 3.9 0.5 - - - -
913D SER* 3.1 41.7 + - - -
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Residues in contact with PHE 907 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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859D ILE* 3.9 3.9 - - - +
860D GLN* 2.9 50.4 + - + -
861D GLY* 2.9 27.0 + - - +
862D PHE* 3.2 32.3 - - - -
863D TYR* 3.3 53.8 - + + -
881D VAL* 4.1 17.3 - - + -
906D CYS* 1.3 75.5 - - - +
908D ASN* 1.3 68.4 + - - +
911D GLY 3.6 11.0 - - - +
912D GLU* 4.1 6.5 - - + -
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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