Contacts of the strand formed by residues 284 - 295 (chain 5) in PDB entry 1SVA
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 ARG 284 (chain 5).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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505 PHE* 3.0 6.1 - - - +
515 LEU* 2.9 33.8 + - + +
1175 THR* 2.7 24.6 + - - -
1185 GLU* 3.4 11.1 - - - +
1195 VAL* 4.0 13.9 - - - +
1205 ILE* 3.5 5.6 - - - -
1505 HIS* 4.7 8.1 - - - +
1515 PHE* 4.1 6.4 + - - +
1525 PHE* 4.0 22.5 - - - -
2635 ALA* 4.3 7.5 - - + +
2655 ASP* 2.7 49.5 + - - +
2835 PRO* 1.3 74.8 - - - +
2855 TYR* 1.3 66.9 + - - +
2865 PHE* 3.0 36.9 - - + -
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Residues in contact with TYR 285 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2121 PRO* 3.1 41.3 + - + -
2131 SER* 3.1 32.3 - - - -
485 GLU* 2.7 33.0 + - + +
495 CYS 3.5 10.5 - - - -
505 PHE* 4.2 2.9 - - + -
1165 LYS* 3.7 11.0 - - + -
1175 THR* 2.9 33.6 - - - -
1185 GLU* 2.8 18.2 + - + +
1205 ILE* 3.3 10.9 - - + +
2845 ARG* 1.3 74.6 - - - +
2865 PHE* 1.3 88.8 + - - +
2875 LYS* 3.3 32.7 - - + +
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Residues in contact with PHE 286 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475 VAL 3.1 3.6 - - - +
485 GLU* 3.2 2.1 - - - -
495 CYS* 2.9 42.9 + - - -
505 PHE* 4.2 4.9 - - - -
515 LEU* 4.0 8.3 - - + -
1155 VAL* 4.5 6.5 - - + -
1165 LYS 3.4 4.9 - - - -
1175 THR* 4.7 0.9 - - + -
1525 PHE* 4.1 19.5 - + - -
1545 VAL* 4.3 9.6 - - + -
2615 VAL* 3.5 40.6 - - + -
2625 SER 4.2 2.0 - - - -
2635 ALA* 3.9 13.7 - - + -
2845 ARG* 3.0 51.8 - - + -
2855 TYR* 1.3 94.1 - - - +
2875 LYS* 1.3 60.1 + - - +
2885 ILE* 3.3 20.0 - - + -
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Residues in contact with LYS 287 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2121 PRO 5.7 0.2 - - - +
2161 GLU* 4.9 10.7 + - - +
2471 GLU* 6.0 0.4 + - - -
465 GLU* 3.1 41.2 + - + -
475 VAL 3.4 4.9 - - - +
485 GLU* 4.1 22.6 + - + +
1145 THR* 3.4 2.1 - - - +
1155 VAL* 3.2 4.7 - - - -
1165 LYS* 2.9 61.8 + - + +
2855 TYR* 3.3 32.1 - - + +
2865 PHE* 1.3 72.0 - - - +
2885 ILE* 1.3 61.3 + - - +
2895 THR* 3.8 6.1 + - - +
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Residues in contact with ILE 288 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455 THR 3.8 0.5 - - - +
465 GLU* 3.4 2.1 - - - -
475 VAL* 2.8 40.3 + - + +
495 CYS* 5.0 2.7 - - - -
935 ILE* 5.8 1.1 - - + -
1125 ALA* 4.2 11.4 - - + -
1145 THR 3.3 8.1 - - - +
1155 VAL* 4.2 10.3 - - + -
1545 VAL* 4.5 14.8 - - + -
2445 LEU* 5.1 0.4 - - + -
2595 LEU* 4.0 20.0 - - + -
2615 VAL* 4.4 9.2 - - + -
2865 PHE* 3.3 39.5 - - + -
2875 LYS* 1.3 75.7 - - - +
2895 THR* 1.3 77.3 + - - +
2905 LEU* 3.9 19.2 + - + -
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Residues in contact with THR 289 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445 PHE* 4.2 22.7 - - + -
455 THR 3.4 8.7 - - - +
465 GLU* 4.4 13.5 + - + +
1125 ALA* 3.6 1.2 - - - -
1135 VAL* 2.9 33.0 + - + +
1145 THR* 3.0 37.3 + - + +
2875 LYS* 4.0 5.9 + - - +
2885 ILE* 1.3 77.4 - - - +
2905 LEU* 1.3 64.3 + - - +
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Residues in contact with LEU 290 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355 LEU* 6.4 1.1 - - + -
445 PHE* 3.3 7.4 - - - +
455 THR* 2.8 32.8 + - + +
475 VAL* 3.9 23.8 - - + -
955 LEU* 3.8 21.3 - - + -
1105 TRP* 3.8 22.4 - - + +
1115 GLU* 3.1 4.9 - - - +
1125 ALA* 3.3 37.0 - - + +
1135 VAL* 4.9 0.4 - - - -
2545 CYS* 4.9 3.4 - - - -
2595 LEU* 3.6 26.7 - - + -
2885 ILE* 3.9 8.1 - - + -
2895 THR* 1.3 75.3 - - - +
2915 ARG* 1.3 60.8 + - - +
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Residues in contact with ARG 291 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435 SER 4.7 1.6 - - - +
445 PHE* 4.2 13.7 - - + -
1105 TRP* 3.3 12.0 - - - -
1115 GLU* 2.8 73.5 + - - +
1135 VAL* 3.7 23.7 - - + +
2455 LEU* 3.6 20.6 - - - +
2495 GLY 3.9 3.2 + - - -
2905 LEU* 1.3 74.4 - - - +
2925 LYS* 1.3 66.7 + - - +
2935 ARG* 3.4 13.9 - - - +
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Residues in contact with LYS 292 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154 LYS* 4.5 7.4 - - - +
395 THR* 2.7 36.4 + - - +
405 GLY 2.5 30.8 + - - +
415 VAL* 3.3 33.1 + - + +
435 SER* 3.8 13.9 + - - +
985 ILE* 3.9 27.1 - - + -
1085 LEU* 4.9 9.9 - - + +
1095 MET 3.9 3.8 - - - -
1105 TRP* 3.6 28.5 - - + -
2915 ARG* 1.3 80.7 - - - +
2935 ARG* 1.3 59.8 + - - +
2945 SER 4.0 1.6 + - - -
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Residues in contact with ARG 293 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204 PRO* 6.1 0.2 - - - -
214 VAL* 3.5 32.3 - - - +
1085 LEU* 3.2 7.1 - - - -
1095 MET 2.8 43.8 + - - +
1115 GLU* 2.3 67.8 + - + +
2485 GLN 4.7 1.2 + - - -
2495 GLY 3.1 19.8 + - - -
2505 VAL* 3.7 15.9 - - + +
2535 LEU* 4.5 9.4 - - + -
2915 ARG* 3.4 15.3 + - - +
2925 LYS* 1.3 73.0 - - - +
2945 SER* 1.3 83.7 + - - +
2955 VAL* 3.5 11.6 + - + +
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Residues in contact with SER 294 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174 PRO* 3.6 15.0 + - - +
184 LYS* 2.6 37.3 + - - -
204 PRO* 3.3 24.0 - - - +
214 VAL 4.8 0.3 + - - -
1055 GLY 5.2 0.9 + - - -
1065 ASN* 5.6 0.3 - - - -
1075 ILE 3.5 7.9 + - - -
1085 LEU* 3.5 9.5 - - - +
2925 LYS 4.0 1.8 + - - -
2935 ARG* 1.3 89.5 + - - +
2955 VAL* 1.3 63.5 + - - +
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Residues in contact with VAL 295 (chain 5).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204 PRO* 3.5 11.8 - - - +
1055 GLY 3.0 20.3 - - - +
1075 ILE* 2.9 38.5 + - + +
1095 MET* 3.6 36.3 - - + -
2535 LEU* 4.0 26.5 - - + -
2935 ARG* 4.0 10.8 - - + +
2945 SER* 1.3 76.3 + - - +
2965 LYS* 1.3 65.1 + - - +
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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