Contacts of the strand formed by residues 991 - 998 (chain D) in PDB entry 5NSS
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 THR 991 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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824D PRO* 4.8 8.6 - - - +
826D ILE* 3.7 34.1 - - - +
878D ASP* 5.3 6.9 - - - +
983D LYS* 5.6 6.3 - - - -
984D LEU 4.1 5.2 - - - -
985D ILE* 5.2 1.8 - - - +
989D GLY 3.7 3.0 + - - -
990D ARG* 1.3 73.8 - - - +
992D LYS* 1.3 63.1 + - - +
993D GLU 5.3 0.2 - - - -
994D SER* 5.4 2.9 - - - -
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Residues in contact with LYS 992 (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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826D ILE* 3.3 21.8 - - - +
831D VAL* 4.3 10.4 - - - +
953D LYS* 4.0 6.6 - - + +
954D ASN* 3.8 38.6 - - + +
984D LEU* 3.1 21.3 + - + +
986D ASP* 5.5 2.7 - - + +
990D ARG 3.4 3.9 + - - +
991D THR* 1.3 71.7 - - - +
993D GLU* 1.3 63.9 + - - +
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Residues in contact with GLU 993 (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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826D ILE* 4.2 5.2 - - - -
828D GLY 3.7 22.9 - - - +
829D GLY 4.2 0.7 - - - +
830D ASP 5.9 0.2 - - - -
831D VAL* 5.9 1.6 - - - +
951D GLN 4.7 7.1 - - - +
952D VAL* 4.7 2.5 - - - -
953D LYS* 3.7 28.5 - - + +
982D LEU 3.9 1.3 - - - +
983D LYS* 3.4 1.9 - - - -
984D LEU* 3.0 26.8 + - + +
991D THR* 6.0 0.2 - - - -
992D LYS* 1.3 81.3 - - - +
994D SER* 1.3 61.6 + - - +
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Residues in contact with SER 994 (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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825D VAL 4.9 0.3 - - - +
826D ILE* 2.9 48.4 + - - +
827D GLU* 3.8 7.8 - - - +
828D GLY 6.0 0.2 - - - -
981D GLU* 6.2 2.5 - - - -
982D LEU 3.2 5.6 - - - -
983D LYS* 3.6 21.1 - - - -
991D THR* 5.4 0.9 - - - -
993D GLU* 1.3 74.3 - - - +
995D TYR* 1.3 61.6 + - - +
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Residues in contact with TYR 995 (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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827D GLU* 4.7 15.7 - - - +
828D GLY* 5.5 5.6 - - - +
946D ALA* 3.9 26.9 - - + -
981D GLU* 4.7 1.8 - - - -
982D LEU* 2.8 38.4 + - + +
993D GLU 4.3 0.4 - - - -
994D SER* 1.3 75.6 - - - +
996D LYS* 1.3 63.0 + - - +
997D VAL 3.3 0.2 + - - -
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Residues in contact with LYS 996 (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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827D GLU* 5.6 0.2 + - - -
946D ALA* 4.7 9.0 - - - +
979D ASN* 6.3 1.8 - - + -
980D THR 3.3 14.4 - - - +
981D GLU* 4.3 2.5 - - - +
995D TYR* 1.3 74.4 - - - +
997D VAL* 1.3 62.0 + - - +
998D PRO* 3.6 3.7 - - - +
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Residues in contact with VAL 997 (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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960D LEU* 5.9 2.2 - - + -
975D ILE* 5.5 3.4 - - + -
978D ARG 3.5 0.5 - - - +
980D THR* 2.9 57.2 + - - -
981D GLU 4.1 2.5 - - - +
982D LEU* 4.1 21.8 - - + -
995D TYR 3.3 1.8 + - - -
996D LYS* 1.3 71.2 - - - +
998D PRO* 1.3 65.1 - - - +
1001D ALA* 5.7 5.2 - - + -
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Residues in contact with PRO 998 (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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975D ILE* 4.8 5.5 - - - +
978D ARG 3.6 5.6 - - - +
979D ASN* 5.3 1.3 - - - -
980D THR 5.0 0.2 - - - +
996D LYS* 3.6 5.9 - - - +
997D VAL* 1.3 76.5 - - - +
999D TYR* 1.3 69.8 - - - +
1000D GLY 3.5 1.6 + - - -
1001D ALA* 3.7 18.6 + - - +
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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