Contacts of the strand formed by residues 107 - 119 (chain 4) 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 4).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
974 ASN* 5.8 0.4 - - - +
994 ASN* 2.8 22.7 - - + +
1024 LEU* 6.4 0.4 - - + -
1034 THR 5.3 8.1 - - - +
1054 GLY 5.3 1.8 - - - +
1064 ASN* 1.3 83.8 - - - +
1084 LEU* 1.3 90.0 + - - +
1094 MET* 4.4 10.3 - - + -
2944 SER* 3.4 2.4 + - - -
2954 VAL* 2.9 41.2 + - + +
2974 ASN* 4.7 20.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 108 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173 PRO* 4.3 20.2 - - + -
414 VAL* 4.5 20.4 - - + -
974 ASN* 4.9 1.7 - - - +
984 ILE* 3.1 38.1 + - + +
994 ASN* 2.5 23.0 + - - +
1064 ASN 5.4 0.7 - - - +
1074 ILE* 1.3 93.2 - - - +
1094 MET* 1.3 63.2 + - - +
2574 ASP* 5.2 2.8 - - - +
2924 LYS* 4.2 20.2 - - + +
2934 ARG* 3.0 14.4 - - - +
2944 SER* 3.5 15.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 109 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
984 ILE* 4.2 5.4 - - - -
1074 ILE* 4.4 9.0 - - + -
1084 LEU* 1.3 78.6 - - - +
1104 TRP* 1.3 69.1 + - - +
1114 GLU 3.2 0.5 + - - -
2534 LEU* 4.3 20.4 - - + -
2544 CYS 3.7 6.3 - - - +
2554 LYS* 3.4 43.5 - - + +
2574 ASP* 5.1 4.3 - - - +
2914 ARG 3.4 0.9 - - - +
2924 LYS* 3.7 0.3 - - - -
2934 ARG* 2.7 38.6 + - - +
2954 VAL* 3.3 39.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 110 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354 LEU* 4.9 7.0 - - + -
394 THR* 5.2 2.0 - - - -
434 SER* 5.1 1.8 - - - -
444 PHE* 5.2 1.3 - - - -
454 THR* 3.7 27.8 - - + -
954 LEU* 3.2 45.0 - - + +
964 PRO* 2.9 40.1 + - + +
984 ILE* 3.1 33.2 - - + +
1094 MET* 1.3 73.5 - - - +
1114 GLU* 1.3 58.0 + - - +
2534 LEU* 3.5 2.4 - - - -
2544 CYS* 2.6 46.1 + - + -
2574 ASP* 4.4 10.9 + - + -
2904 LEU* 3.7 27.1 - - + -
2914 ARG* 3.6 21.5 - - - -
2924 LYS* 4.1 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 111 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1094 MET 3.2 0.8 + - - -
1104 TRP* 1.3 71.9 - - - +
1124 ALA* 1.3 72.7 + - - +
1134 VAL* 3.7 3.1 + - + +
2454 LEU* 4.0 0.5 - - - +
2504 VAL* 3.0 3.6 - - - -
2514 GLY 2.6 26.7 + - - +
2524 PRO 3.4 7.0 - - - +
2534 LEU* 3.9 12.3 - - + -
2904 LEU* 3.0 10.1 - - - +
2914 ARG* 2.7 76.6 + - + +
2934 ARG* 2.4 46.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 112 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1104 TRP 4.1 0.8 + - - -
1114 GLU* 1.3 75.0 - - - +
1134 VAL* 1.3 60.1 + - - +
1544 VAL* 4.3 6.5 - - + -
2444 LEU* 4.0 12.8 - - + -
2514 GLY* 3.0 26.5 - - - -
2524 PRO* 2.9 32.2 + - + +
2544 CYS* 5.2 1.3 - - - -
2594 LEU* 5.0 7.6 - - + -
2884 ILE* 4.2 9.0 - - + -
2894 THR 3.8 0.7 - - - -
2904 LEU* 3.3 17.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 113 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1114 GLU* 3.8 12.1 - - + +
1124 ALA* 1.3 80.0 - - - +
1144 THR* 1.3 72.0 + - - +
2434 VAL* 3.6 4.6 - - + +
2444 LEU* 2.7 32.2 + - - -
2454 LEU* 3.8 20.4 - - + +
2894 THR* 3.0 14.0 + - + +
2914 ARG* 3.6 43.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 114 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1134 VAL* 1.3 93.3 + - - +
1154 VAL* 1.3 69.1 + - - +
1164 LYS* 4.9 3.8 - - + -
2414 THR* 3.2 28.0 - - + +
2424 THR 3.2 9.2 + - - -
2434 VAL* 4.4 5.9 - - - +
2444 LEU* 3.4 5.5 - - - +
2874 LYS 4.5 1.6 - - - +
2884 ILE* 3.2 4.9 - - - +
2894 THR* 2.9 50.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 115 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1144 THR* 1.3 78.3 - - - +
1164 LYS* 1.3 74.7 + - - +
1174 THR* 4.7 3.1 - - + -
1524 PHE* 4.3 18.4 - - + -
1544 VAL* 4.1 14.1 - - + -
2414 THR* 3.7 1.2 - - - +
2424 THR* 2.8 57.3 + - + +
2444 LEU* 4.0 19.1 - - + -
2864 PHE* 4.2 11.7 - - + -
2874 LYS 3.2 6.1 - - - +
2884 ILE* 4.0 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 116 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1144 THR* 4.9 2.7 - - + -
1154 VAL* 1.3 79.5 - - - +
1174 THR* 1.3 63.1 + - - +
2384 ASN* 3.7 25.6 + - - +
2394 THR 5.0 3.2 + - - -
2404 ALA 3.5 26.0 - - - +
2414 THR* 3.6 26.0 - - + +
2424 THR* 5.7 0.4 - - - -
2854 TYR* 4.6 6.7 - - + -
2864 PHE* 3.3 2.6 - - - -
2874 LYS* 2.9 63.6 + - + +
2475 GLU* 2.9 29.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 117 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1154 VAL* 4.7 3.4 - - + -
1164 LYS* 1.3 76.2 - - - +
1184 GLU* 1.3 73.0 + - - +
1524 PHE* 3.8 33.7 - - + -
2374 THR 5.1 2.3 - - - +
2404 ALA 4.9 2.8 + - - +
2424 THR* 5.7 3.1 - - - +
2844 ARG* 2.7 33.1 + - - +
2854 TYR* 2.7 23.1 + - - -
2864 PHE* 4.6 8.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 118 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1174 THR* 1.3 84.1 + - - +
1194 VAL* 1.3 68.0 + - - +
1204 ILE* 3.5 0.6 + - + -
2354 HIS 3.9 6.5 - - - +
2364 ILE* 2.8 43.2 - - + +
2374 THR 2.8 36.2 + - - +
2384 ASN* 4.4 0.9 - - - -
2844 ARG* 3.4 6.9 - - - +
2854 TYR* 2.9 39.8 + - + +
2125 PRO* 4.1 13.8 - - + +
2205 TYR* 2.6 20.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 119 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1184 GLU* 1.3 78.1 - - - +
1204 ILE* 1.3 66.3 + - - +
1214 GLY 3.4 3.1 + - - -
1224 VAL* 3.7 18.1 - - + +
1504 HIS* 4.8 4.9 - - + +
2344 LEU* 4.9 16.4 - - + -
2354 HIS 5.0 3.4 + - - +
2364 ILE* 3.6 19.4 - - - +
2654 ASP* 3.4 30.3 - - + +
2674 CYS* 4.9 2.2 - - - -
2824 LEU* 3.3 40.2 - - + -
2834 PRO 3.7 3.6 - - - +
2844 ARG* 4.0 13.7 - - + +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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