Contacts of the strand formed by residues 102 - 110 (chain 0) in PDB entry 5IY8
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 102 (chain 0).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580 MET* 4.2 0.4 - - - +
590 ARG* 3.2 22.7 - - - +
950 TYR* 3.3 31.4 - - - -
960 PHE* 3.4 13.3 - - - -
990 ASN* 2.6 23.5 + - - -
1000 PRO 3.6 2.7 + - - +
1010 ILE* 1.3 76.0 - - - +
1030 GLN* 1.3 76.9 + - - +
1220 GLY* 3.4 17.5 - - - +
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Residues in contact with GLN 103 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580 MET* 3.5 23.3 - - - +
590 ARG 2.7 14.1 + - - +
600 HIS* 3.2 43.3 + - + +
610 LEU 3.0 23.4 + - - -
950 TYR* 3.4 5.0 + - - -
960 PHE* 4.3 2.5 - - - -
1010 ILE* 5.7 0.2 - - - +
1020 SER* 1.3 84.1 + - - +
1040 ILE* 1.3 68.1 + - - +
1200 LEU* 3.8 17.3 - - + -
1210 SER* 3.2 22.7 - - - +
1220 GLY* 4.0 3.6 + - - +
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Residues in contact with ILE 104 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610 LEU* 3.1 24.7 - - + +
630 VAL* 3.7 18.2 - - + -
910 PHE* 4.6 7.0 - - + -
920 VAL* 5.0 10.3 - - + -
950 TYR* 3.5 39.5 - - + +
960 PHE* 3.9 14.5 - - + -
1030 GLN* 1.3 78.5 - - - +
1050 GLY* 1.3 71.0 + - - +
1060 ILE* 4.1 3.8 - - + -
1200 LEU* 3.3 6.9 - - - -
1210 SER 3.0 21.0 + - - -
1270 HIS* 2.8 44.1 + - + +
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Residues in contact with GLY 105 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610 LEU 3.1 6.5 + - - -
620 TYR* 3.4 21.2 - - - -
630 VAL 3.0 24.4 + - - -
1040 ILE* 1.3 74.8 - - - +
1060 ILE* 1.4 65.1 + - - +
1180 THR 3.6 10.1 - - - -
1190 GLU 4.0 0.7 - - - -
1200 LEU* 3.7 14.2 - - - +
1270 HIS* 4.6 0.4 - - - -
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Residues in contact with ILE 106 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620 TYR* 4.5 0.6 - - - -
630 VAL* 3.4 23.3 - - + +
650 VAL* 5.0 4.5 - - + -
920 VAL* 5.3 1.6 - - + -
1040 ILE* 4.1 6.5 - - + -
1050 GLY* 1.4 76.9 - - - +
1070 ILE* 1.3 65.1 + - - +
1160 LYS* 3.6 4.5 - - - +
1170 LEU* 2.9 45.1 + - + -
1180 THR* 2.9 45.2 + - - +
1270 HIS* 3.6 39.9 - - + +
1300 SER* 4.6 2.0 - - - -
1310 LEU* 4.4 22.2 - - + -
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Residues in contact with ILE 107 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620 TYR* 3.7 31.0 - - + -
630 VAL 3.0 12.2 + - - +
640 VAL* 3.3 11.2 - - + -
650 VAL* 3.1 25.1 + - - +
1060 ILE* 1.3 77.3 - - - +
1080 VAL* 1.3 72.2 + - - +
1140 ALA* 4.4 5.4 - - + -
1150 GLU 3.3 11.4 - - - +
1160 LYS* 4.6 7.4 - - + -
1170 LEU* 4.5 1.6 - - - -
1480 SER* 3.7 44.9 - - - +
1510 ILE* 3.9 24.5 - - + -
1520 ALA* 4.2 3.1 - - + +
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Residues in contact with VAL 108 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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640 VAL* 5.5 0.4 - - - -
650 VAL* 3.5 22.7 - - + +
670 GLY* 4.0 18.4 - - - +
1070 ILE* 1.3 78.1 - - - +
1090 THR* 1.4 69.6 + - - +
1100 LYS* 4.2 10.7 + - + -
1130 ARG 3.7 0.2 - - - +
1140 ALA* 3.3 4.2 - - - -
1150 GLU* 2.9 54.7 + - + +
1170 LEU* 3.7 31.4 - - + -
1370 MET* 4.5 12.8 - - + -
1380 THR 6.0 0.4 - - - +
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Residues in contact with THR 109 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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640 VAL* 4.7 5.7 - - + +
650 VAL 3.0 13.4 + - - -
660 ASP* 3.8 9.0 + - - +
670 GLY* 2.7 32.6 + - - -
680 SER* 3.5 2.4 + - - -
1080 VAL* 1.4 70.0 - - - +
1100 LYS* 1.3 58.1 + - - +
1130 ARG 3.2 4.3 - - - +
1420 GLU 4.5 2.5 - - - -
1430 PRO* 3.6 13.1 - - - +
1440 SER* 3.2 37.0 - - - +
1450 LEU* 3.9 12.5 - - + +
1480 SER* 3.0 31.2 - - - +
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Residues in contact with LYS 110 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670 GLY* 3.5 20.9 - - - +
1080 VAL* 4.2 10.2 + - + -
1090 THR* 1.3 75.3 - - - +
1110 SER* 1.3 86.3 + - - +
1120 LYS 3.2 2.7 - - - -
1130 ARG* 2.9 24.1 + - - +
1150 GLU* 6.5 0.2 - - + -
1370 MET* 2.9 41.2 + - + +
1380 THR 2.9 31.7 + - - +
1390 CYS* 4.1 4.9 - - - +
1400 HIS* 3.7 8.5 - - - +
1420 GLU 3.8 4.9 + - - -
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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