Contacts of the strand formed by residues 107 - 119 (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 ILE 107 (chain 5).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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995 ASN* 3.0 19.5 - - + +
1015 ASP 5.3 4.3 - - - +
1035 THR 5.4 4.9 - - - +
1045 CYS* 5.7 0.4 - - - -
1055 GLY* 2.9 21.9 + - - +
1065 ASN* 1.3 89.4 - - - +
1085 LEU* 1.3 74.4 + - - +
1095 MET* 4.5 8.7 - - + -
2945 SER* 3.5 2.3 + - - -
2955 VAL* 2.9 49.3 + - + +
2975 ASN* 4.6 20.0 - - + +
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Residues in contact with LEU 108 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154 LYS* 4.8 9.9 - - + +
174 PRO* 3.4 34.8 - - + -
415 VAL* 4.5 18.8 - - + -
975 ASN* 5.5 0.2 + - - -
985 ILE* 3.3 41.6 + - + +
995 ASN* 2.7 27.4 + - - +
1015 ASP* 4.0 16.8 - - - +
1075 ILE* 1.3 83.3 - - - +
1095 MET* 1.3 64.7 + - - +
2575 ASP* 5.1 3.5 - - - +
2925 LYS* 4.9 7.6 - - + +
2935 ARG* 3.2 7.6 - - - +
2945 SER* 3.5 17.7 - - - +
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Residues in contact with MET 109 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
985 ILE* 4.6 4.5 - - - -
1075 ILE* 4.5 8.3 - - + -
1085 LEU* 1.3 76.8 - - - +
1105 TRP* 1.3 66.3 + - - +
1115 GLU 3.3 0.5 + - - -
2535 LEU* 4.7 15.7 - - + -
2545 CYS 3.6 11.2 - - - +
2555 LYS* 3.4 45.1 - - + +
2575 ASP* 5.3 3.8 - - - +
2915 ARG 3.6 0.3 - - - +
2925 LYS* 3.8 1.0 - - - -
2935 ARG* 2.8 37.0 + - - +
2955 VAL* 3.6 38.4 - - + -
2965 LYS 5.3 3.8 - - - +
2985 PRO* 6.2 3.4 - - + -
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Residues in contact with TRP 110 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355 LEU* 5.0 7.4 - - + -
395 THR* 5.6 0.4 - - - -
435 SER* 5.0 2.0 - - - -
445 PHE* 5.2 1.6 - - - -
455 THR* 4.1 20.4 - - + -
955 LEU* 3.0 50.6 - - + +
965 PRO* 3.2 35.0 + - + +
985 ILE* 3.1 22.9 - - + +
1095 MET* 1.3 73.3 - - - +
1115 GLU* 1.3 59.1 + - - +
2535 LEU* 3.6 1.3 - - - -
2545 CYS* 2.8 46.5 + - + -
2575 ASP* 4.9 8.9 + - + -
2905 LEU* 3.8 20.4 - - + -
2915 ARG* 3.3 22.9 - - - -
2925 LYS* 3.6 35.2 - - + -
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Residues in contact with GLU 111 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1095 MET 3.3 1.0 + - - -
1105 TRP* 1.3 72.6 - - - +
1125 ALA* 1.3 72.5 + - - +
1135 VAL* 3.4 3.4 - - + +
2455 LEU* 4.0 1.0 - - - +
2505 VAL* 3.0 5.3 - - - -
2515 GLY 2.6 24.8 + - - +
2525 PRO 3.4 10.3 - - - +
2535 LEU* 3.5 14.1 - - + -
2905 LEU* 3.1 5.5 - - - -
2915 ARG* 2.8 69.9 + - + +
2935 ARG* 2.3 47.1 + - + +
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Residues in contact with ALA 112 (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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1105 TRP 4.0 1.0 + - - -
1115 GLU* 1.3 72.2 - - - +
1135 VAL* 1.3 60.9 + - - +
1545 VAL* 4.4 8.5 - - + -
2445 LEU* 4.0 8.2 - - + +
2515 GLY* 3.1 26.5 - - - -
2525 PRO* 2.9 30.8 + - + +
2545 CYS* 5.3 1.7 - - - -
2595 LEU* 4.9 4.9 - - + -
2885 ILE* 4.2 11.2 - - + -
2895 THR 3.6 0.4 - - - -
2905 LEU* 3.3 22.0 - - + +
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Residues in contact with VAL 113 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1115 GLU* 3.4 17.3 - - + +
1125 ALA* 1.3 80.4 - - - +
1145 THR* 1.3 69.8 + - - +
2435 VAL* 3.5 2.8 - - + +
2445 LEU* 2.7 33.7 + - - -
2455 LEU* 3.3 24.5 - - + +
2895 THR* 2.9 16.0 + - + +
2905 LEU 4.9 0.2 - - - -
2915 ARG* 3.7 41.1 - - + +
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Residues in contact with THR 114 (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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1135 VAL* 1.3 90.9 + - - +
1155 VAL* 1.3 69.7 + - - +
1165 LYS* 4.7 4.7 - - + +
2415 THR* 3.2 27.1 - - + +
2425 THR 3.2 7.7 + - - -
2435 VAL* 4.4 7.4 - - - +
2445 LEU* 3.1 5.8 - - - +
2875 LYS 4.5 1.6 - - - +
2885 ILE* 3.3 4.5 - - - +
2895 THR* 3.0 50.8 + - - +
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Residues in contact with VAL 115 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1145 THR* 1.3 80.7 - - - +
1165 LYS* 1.3 75.3 + - - +
1175 THR* 3.6 13.6 - - + +
1525 PHE* 4.4 15.7 - - + -
1545 VAL* 4.4 10.3 - - + -
2425 THR* 2.7 54.4 + - + +
2445 LEU* 3.9 22.4 - - + -
2865 PHE* 4.5 2.5 - - + -
2875 LYS 3.2 8.5 - - - +
2885 ILE* 4.2 20.0 - - + -
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Residues in contact with LYS 116 (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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2471 GLU* 3.2 31.0 + - - -
1145 THR* 4.9 3.4 - - + -
1155 VAL* 1.3 75.9 - - - +
1175 THR* 1.3 66.1 + - - +
2385 ASN* 3.5 28.3 + - + +
2395 THR* 5.0 2.8 - - - +
2405 ALA 3.6 22.2 - - - +
2415 THR* 3.4 26.0 + - + +
2855 TYR* 3.7 5.8 - - + -
2865 PHE* 3.4 1.0 - - - -
2875 LYS* 2.9 66.8 + - + +
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Residues in contact with THR 117 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1155 VAL* 3.6 20.6 - - + +
1165 LYS* 1.3 80.1 - - - +
1185 GLU* 1.3 65.8 + - - +
1525 PHE* 3.7 29.9 - - + -
2375 THR 5.0 2.6 - - - +
2405 ALA 4.9 2.5 + - - +
2425 THR* 5.7 1.8 - - - +
2845 ARG* 2.7 29.4 + - - +
2855 TYR* 2.9 24.5 - - - +
2865 PHE* 4.6 2.7 - - + -
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Residues in contact with GLU 118 (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* 4.1 12.8 - - + +
2201 TYR* 2.7 20.5 + - - -
1175 THR* 1.3 81.0 + - - +
1195 VAL* 1.3 67.3 + - - +
1205 ILE* 3.3 4.1 - - + +
2355 HIS 4.3 4.9 - - - +
2365 ILE* 2.8 48.3 - - + +
2375 THR 2.5 38.0 + - - +
2845 ARG* 3.4 5.5 - - - +
2855 TYR* 2.8 37.5 + - + +
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Residues in contact with VAL 119 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1185 GLU* 1.3 76.1 - - - +
1205 ILE* 1.3 68.7 + - - +
1225 VAL* 3.6 6.9 - - + +
1505 HIS* 4.6 8.1 - - + +
2345 LEU* 4.7 21.8 - - + -
2355 HIS 5.5 1.4 + - - -
2365 ILE* 3.4 22.2 - - - +
2655 ASP* 3.5 28.0 - - + +
2675 CYS* 4.8 2.7 - - - -
2825 LEU* 3.4 37.2 - - + -
2835 PRO 3.5 5.2 - - - +
2845 ARG* 4.0 14.6 - - - +
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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
------------------------------------------------------------
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