Contacts of the strand formed by residues 987 - 996 (chain I) in PDB entry 4XLN
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 ILE 987 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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675I ALA* 4.2 0.2 - - + -
676I ILE 3.2 24.7 - - - +
677I MET* 3.5 39.0 - - + -
971I LYS* 4.0 3.4 - - - -
972I VAL* 3.2 23.2 + - - +
974I LEU* 3.7 22.6 - - + +
983I PHE* 3.6 36.6 - - + -
985I GLY 3.9 3.1 - - - +
986I PRO* 1.3 79.4 - - - +
988I VAL* 1.3 71.5 + - - +
989I VAL* 3.3 10.9 + - + +
946J GLY* 3.7 14.1 - - - +
948J THR* 3.8 3.1 - - - -
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Residues in contact with VAL 988 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676I ILE* 2.9 46.1 + - + +
885I ILE* 5.7 1.6 - - + -
888I THR* 4.9 4.3 - - + -
889I HIS* 4.4 8.7 - - + -
969I LEU 4.5 0.9 - - - +
970I GLY 3.2 15.0 - - - +
971I LYS* 3.5 28.5 - - + +
987I ILE* 1.3 69.8 - - - +
989I VAL* 1.3 61.1 + - - +
948J THR* 3.0 29.5 + - + +
949J ILE 3.4 16.4 - - - +
950J GLY* 3.7 21.5 - - - -
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Residues in contact with VAL 989 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673I LEU* 4.0 10.5 - - + -
674I VAL 3.0 10.3 - - - +
675I ALA* 3.6 22.4 - - + -
861I LEU* 5.2 8.1 - - + -
867I VAL* 4.6 3.8 - - + -
888I THR* 3.4 15.3 - - - +
889I HIS* 5.3 0.5 + - - -
892I LEU* 3.4 35.5 - - + +
970I GLY* 3.3 4.5 + - - +
972I VAL* 3.6 21.3 - - + -
974I LEU* 3.9 18.4 - - + -
987I ILE* 3.3 11.9 + - + +
988I VAL* 1.3 80.1 - - - +
990I GLY* 1.3 60.6 + - - +
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Residues in contact with GLY 990 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673I LEU* 3.3 15.8 - - - +
674I VAL* 2.9 31.0 + - - +
888I THR* 3.6 12.5 - - - +
892I LEU* 3.8 14.8 - - - -
895I TYR* 6.1 0.9 - - - -
989I VAL* 1.3 80.8 - - - +
991I GLN* 1.3 63.8 + - - -
992I MET 3.4 0.3 + - - -
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Residues in contact with GLN 991 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575I GLN* 5.3 4.9 - - - +
578I VAL* 3.8 29.5 - - + +
579I VAL* 5.5 0.2 - - - +
671I ASN* 4.7 15.1 + - + +
672I VAL 3.2 14.3 - - - +
673I LEU* 5.2 3.1 - - + -
887I GLU* 2.9 24.3 - - - +
888I THR* 4.4 0.9 - - - -
891I GLY* 3.2 25.1 - - - +
894I GLY* 3.4 6.8 - - - +
895I TYR* 3.2 49.6 + - + +
990I GLY* 1.3 70.1 - - - -
992I MET* 1.3 59.9 + - - +
993I PHE 4.3 0.2 + - - -
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Residues in contact with MET 992 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671I ASN* 4.3 2.7 - - - -
672I VAL 2.9 29.4 + - - +
674I VAL* 3.7 23.1 - - + -
676I ILE* 5.0 4.9 - - + -
841I ASN* 3.4 22.4 - - - +
871I LEU* 4.1 15.7 - - + -
884I GLN* 3.8 22.9 - - + +
887I GLU* 3.2 23.8 - - + +
888I THR* 3.2 26.5 - - - +
990I GLY 3.4 1.4 + - - -
991I GLN* 1.3 74.6 - - - +
993I PHE* 1.3 63.3 + - - +
994I ILE* 3.4 31.9 + - + +
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Residues in contact with PHE 993 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575I GLN 3.6 9.9 - - - -
577I PRO* 3.5 29.8 - - + -
579I VAL* 5.9 0.4 - - + +
668I LEU* 3.6 23.3 - - + -
669I GLY* 3.2 44.0 - - - -
670I GLN 3.8 4.7 - - - -
671I ASN* 3.3 21.3 + - - +
841I ASN* 3.5 21.0 - - - +
842I ARG* 3.3 44.1 + - + +
887I GLU* 3.3 22.1 + - - +
991I GLN 4.3 0.4 + - - -
992I MET* 1.3 72.7 - - - +
994I ILE* 1.3 60.3 + - - +
995I MET* 4.9 8.3 - - + -
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Residues in contact with ILE 994 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669I GLY* 3.2 1.6 - - - -
670I GLN 2.9 23.2 + - - -
672I VAL* 3.7 17.7 - - + -
674I VAL* 4.8 0.4 - - + -
688I ILE* 5.8 2.9 - - + -
700I TYR* 2.6 34.9 + - + +
839I LEU* 4.7 11.7 - - + -
840I ALA* 3.4 18.4 - - - +
841I ASN* 4.7 1.3 - - + -
869I VAL* 4.0 23.8 - - + -
871I LEU* 4.5 7.9 - - + -
992I MET* 3.6 35.2 - - + +
993I PHE* 1.3 82.1 - - - +
995I MET* 1.3 69.0 + - - +
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Residues in contact with MET 995 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564I MET 5.5 1.1 - - - +
565I GLN* 5.8 0.2 - - - -
568I ALA* 3.5 20.6 - - + -
569I VAL 3.2 28.9 - - - +
571I LEU* 3.8 4.7 - - + -
668I LEU* 3.3 52.0 - - + +
669I GLY* 3.7 3.8 - - - +
700I TYR* 4.0 2.9 - - - -
839I LEU* 3.4 5.5 - - - +
840I ALA* 2.4 60.2 + - + +
841I ASN* 4.5 4.2 - - - +
842I ARG* 6.5 0.2 - - + -
993I PHE* 4.9 5.2 - - + -
994I ILE* 1.3 70.0 - - - +
996I LYS* 1.3 99.4 + - - +
997I LEU* 3.6 8.7 + - + -
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Residues in contact with LYS 996 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569I VAL* 3.2 28.6 + - + +
571I LEU* 4.6 7.6 - - + -
700I TYR* 3.2 45.3 + - + +
702I SER* 4.2 9.0 + - - -
831I ARG 4.7 2.4 + - - -
832I LYS 4.8 0.2 - - - -
833I LEU* 3.7 38.1 - - + +
837I ASP* 4.7 1.8 - - - -
838I LYS 4.0 2.5 - - - +
839I LEU* 3.6 9.0 - - + -
995I MET* 1.3 91.9 - - + +
997I LEU* 1.3 73.2 + - - +
1000I MET* 3.5 43.5 - - - -
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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