Contacts of the strand formed by residues 106 - 120 (chain 6) 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 ASN 106 (chain 6).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3393 GLU* 3.6 24.2 + - - +
996 ASN* 4.1 4.0 + - - -
1036 THR* 5.6 5.4 - - - -
1046 CYS 3.1 11.3 + - - +
1056 GLY* 1.3 84.5 + - - -
1076 ILE* 1.3 66.6 + - - +
1086 LEU* 5.6 0.2 - - - +
2946 SER* 4.5 10.5 - - - +
2956 VAL 3.4 13.6 + - - +
2966 LYS* 3.7 5.3 - - - +
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Residues in contact with ILE 107 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
996 ASN* 2.9 28.0 - - - +
1036 THR* 5.2 6.7 - - + +
1066 ASN* 1.3 78.7 - - - +
1086 LEU* 1.3 84.9 + - - +
1096 MET* 5.2 6.3 - - + -
2946 SER* 3.8 3.5 + - - -
2956 VAL* 3.0 36.4 + - + -
2976 ASN* 3.1 45.3 - - + +
2986 PRO* 3.2 18.8 - - + -
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Residues in contact with LEU 108 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416 VAL* 4.3 27.6 - - + -
986 ILE* 3.0 37.8 + - + +
996 ASN* 2.8 22.5 - - + +
1066 ASN 5.6 0.2 - - - +
1076 ILE* 1.3 82.0 - - - +
1096 MET* 1.3 62.5 + - - +
2576 ASP* 5.2 2.3 - - - +
2926 LYS* 4.4 16.8 - - + +
2936 ARG 3.2 25.8 - - - +
2946 SER* 3.4 22.7 - - - +
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Residues in contact with MET 109 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3423 GLY* 3.2 31.6 - - - +
986 ILE* 4.8 2.9 - - - -
1076 ILE* 5.2 6.5 - - + -
1086 LEU* 1.3 76.5 - - - +
1106 TRP* 1.3 63.0 + - - +
1116 GLU 3.5 0.5 + - - -
2536 LEU* 4.4 13.5 - - + -
2546 CYS 3.5 20.2 - - - +
2556 LYS* 3.7 29.6 - - - +
2576 ASP* 4.6 7.0 - - - +
2916 ARG 3.8 0.2 - - - +
2926 LYS* 3.8 2.4 - - - -
2936 ARG* 2.9 38.1 + - - +
2956 VAL* 3.1 37.7 - - + -
2986 PRO* 5.6 2.7 - - + -
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Residues in contact with TRP 110 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356 LEU* 4.4 10.3 - - + -
396 THR* 5.6 1.1 - - - -
436 SER* 4.8 2.2 - - - -
446 PHE* 4.9 2.0 - - - -
456 THR* 3.8 24.5 - - + -
956 LEU* 3.4 44.0 - - + +
966 PRO* 3.1 36.8 + - + +
986 ILE* 3.1 30.8 - - + +
1096 MET* 1.3 75.1 - - - +
1116 GLU* 1.3 58.9 + - - +
2536 LEU* 3.7 1.9 - - - -
2546 CYS* 2.8 43.2 + - + +
2576 ASP* 4.6 9.5 + - + -
2906 LEU* 3.7 29.2 - - + -
2916 ARG* 3.4 31.2 - - - -
2926 LYS* 4.1 17.3 - - + -
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Residues in contact with GLU 111 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1096 MET 3.5 0.6 + - - -
1106 TRP* 1.3 72.5 - - - +
1126 ALA* 1.3 74.5 + - - +
1136 VAL* 3.6 3.3 - - + +
2456 LEU* 3.4 0.3 - - - +
2506 VAL* 3.0 2.9 - - - -
2516 GLY 2.5 28.2 + - - +
2526 PRO 3.3 7.6 - - - +
2536 LEU* 3.6 11.9 - - + -
2906 LEU* 3.1 8.7 - - - -
2916 ARG* 2.7 70.8 + - + +
2936 ARG* 2.4 49.7 + - + +
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Residues in contact with ALA 112 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1106 TRP 4.1 0.8 + - - -
1116 GLU* 1.3 71.2 - - - +
1136 VAL* 1.3 65.3 + - - +
1546 VAL* 4.4 6.7 - - + -
2446 LEU* 4.0 12.6 - - + -
2516 GLY* 3.0 26.7 - - - -
2526 PRO* 2.9 33.4 + - + +
2546 CYS* 5.4 1.7 - - - -
2596 LEU* 4.7 5.2 - - + -
2886 ILE* 4.2 6.5 - - + -
2896 THR 3.7 0.2 - - - -
2906 LEU* 3.3 20.3 - - + +
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Residues in contact with VAL 113 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1116 GLU* 3.6 15.5 - - + +
1126 ALA* 1.3 83.1 - - - +
1146 THR* 1.3 73.0 + - - +
2436 VAL* 3.5 6.6 - - + +
2446 LEU* 2.7 29.2 + - - -
2456 LEU* 3.8 21.0 + - + -
2896 THR* 3.0 15.4 + - + +
2916 ARG* 3.9 38.4 - - + +
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Residues in contact with THR 114 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1136 VAL* 1.3 90.6 + - - +
1156 VAL* 1.3 69.2 + - - +
1166 LYS* 5.1 2.9 - - + -
2416 THR* 3.2 29.2 - - + +
2426 THR 3.2 6.2 + - - -
2436 VAL* 4.6 6.1 - - - +
2446 LEU* 3.6 3.8 - - - +
2876 LYS* 4.8 1.3 - - + +
2886 ILE* 3.4 6.1 - - - +
2896 THR* 3.0 51.4 + - + +
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Residues in contact with VAL 115 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1146 THR* 1.3 78.9 - - - +
1166 LYS* 1.3 78.0 + - - +
1176 THR* 4.3 4.6 + - - +
1526 PHE* 4.4 14.8 - - + -
1546 VAL* 4.2 17.9 - - + -
2416 THR* 3.8 0.7 - - - +
2426 THR* 2.8 56.9 + - + +
2446 LEU* 3.8 23.8 - - + -
2866 PHE* 4.3 14.6 - - + -
2876 LYS 3.2 7.9 - - - +
2886 ILE* 4.4 6.1 - - + -
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Residues in contact with LYS 116 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1146 THR* 5.1 2.9 - - + -
1156 VAL* 1.3 75.1 - - - +
1176 THR* 1.3 61.0 + - - +
2376 THR 5.8 0.4 - - - +
2386 ASN* 3.0 31.6 + - + +
2396 THR* 4.6 3.3 - - - +
2406 ALA 3.2 28.3 - - - +
2416 THR* 3.2 26.5 - - + +
2856 TYR* 3.7 7.9 - - + +
2866 PHE* 3.2 4.0 - - - -
2876 LYS* 2.8 65.7 + - + +
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Residues in contact with THR 117 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1156 VAL* 4.5 3.6 - - + -
1166 LYS* 1.3 76.1 - - - +
1186 GLU* 1.3 69.4 + - - +
1526 PHE* 3.6 34.1 - - + -
2376 THR 5.3 1.2 - - - +
2406 ALA 5.0 2.8 + - - +
2426 THR* 5.8 2.5 - - - +
2846 ARG* 2.7 34.6 + - - +
2856 TYR* 2.6 22.6 + - - -
2866 PHE* 4.3 10.5 - - - -
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Residues in contact with GLU 118 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1176 THR* 1.3 83.7 + - - +
1196 VAL* 1.3 70.9 + - - +
1206 ILE* 5.9 0.9 - - + -
2356 HIS 4.3 4.9 - - - +
2366 ILE* 2.8 36.7 - - + +
2376 THR* 2.7 48.3 + - - +
2386 ASN* 4.4 1.8 - - - +
2846 ARG* 3.3 7.6 - - - +
2856 TYR* 2.8 42.5 + - + +
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Residues in contact with VAL 119 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1186 GLU* 1.3 80.4 - - - +
1206 ILE* 1.3 67.4 + - - +
1216 GLY 3.2 3.1 + - - -
1226 VAL* 3.5 23.7 - - + +
1506 HIS* 5.1 4.9 - - + +
2346 LEU* 4.4 15.9 - - + -
2356 HIS 5.2 3.8 + - - +
2366 ILE* 3.5 12.7 - - - +
2656 ASP* 4.1 10.1 - - - +
2676 CYS* 5.2 2.0 - - - -
2826 LEU* 3.5 39.9 - - + -
2836 PRO 3.7 4.7 - - - +
2846 ARG* 4.0 25.8 - - - +
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Residues in contact with ILE 120 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506 PHE* 4.4 8.7 - - + -
1186 GLU* 5.0 0.7 - - + -
1196 VAL* 1.3 72.9 - - - +
1216 GLY* 1.3 62.1 + - - +
2366 ILE* 5.1 2.7 - - + -
2826 LEU* 3.4 23.4 - - - +
2836 PRO* 2.7 43.1 + - + +
2846 ARG* 3.2 10.3 - - - +
2856 TYR* 3.2 46.0 - - + +
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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
------------------------------------------------------------
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