Contacts of the helix formed by residues 49 - 66 (chain 4) in PDB entry 3J9X
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 VAL 49 (chain 4).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103 TYR* 3.8 10.5 - - + -
133 ARG* 3.7 26.9 - - - +
454 PHE* 3.0 63.6 + - + +
484 ASN* 1.3 71.1 - - - +
504 PRO* 1.4 61.2 - - + +
514 LYS 3.0 4.0 - - - -
524 PHE* 2.8 30.5 + - + +
534 THR 3.2 6.9 + - - -
3318 A 3.9 28.3 - - + +
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Residues in contact with PRO 50 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103 TYR* 3.5 34.9 - - + -
464 GLN 3.1 26.0 - - - +
474 THR 3.7 6.1 - - - +
484 ASN 3.4 2.5 - - - -
494 VAL* 1.4 96.0 - - + +
514 LYS* 1.3 64.6 + - + +
534 THR* 3.7 5.0 - - - +
544 SER* 3.1 25.1 + - - -
50Y PRO* 5.8 2.5 - - + -
9Z SER* 6.4 2.9 - - - -
10Z TYR* 4.1 20.0 - - + -
11Z SER* 5.7 0.7 - - - -
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Residues in contact with LYS 51 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474 THR* 3.4 28.3 + - - +
484 ASN* 3.0 33.7 + - - +
494 VAL 3.0 0.2 - - - -
504 PRO* 1.3 81.3 - - + +
524 PHE* 1.3 63.1 + - + +
544 SER* 2.9 20.0 + - - -
554 VAL* 3.4 12.7 - - - +
844 ALA* 6.2 0.2 - - - -
884 ASN* 3.8 29.3 + - - +
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Residues in contact with PHE 52 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133 ARG* 4.6 6.3 - - - +
484 ASN* 3.1 29.4 - - + -
494 VAL* 2.8 7.5 + - + +
514 LYS* 1.3 75.4 - - + +
534 THR* 1.3 66.9 + - - +
544 SER 3.2 1.6 - - - -
554 VAL* 3.1 8.1 + - - +
564 ASN* 3.0 26.5 + - - +
814 LEU* 3.5 44.9 - - + -
844 ALA* 3.6 13.7 - - + -
854 ARG* 3.5 14.1 - - - -
884 ASN* 3.4 28.5 - - - -
3308 T 3.6 25.1 - - + +
3318 A 3.5 29.2 - - - +
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Residues in contact with THR 53 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83 ARG 4.8 3.4 - - - +
93 SER* 4.3 5.2 - - - -
103 TYR* 3.5 42.5 - - + +
133 ARG* 2.8 36.8 + - - +
494 VAL 3.2 7.6 + - - -
504 PRO 3.3 7.6 + - - -
524 PHE* 1.3 79.0 - - - +
544 SER* 1.3 62.7 + - - +
564 ASN* 3.1 17.6 + - + +
574 GLU* 3.1 12.8 + - + +
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Residues in contact with SER 54 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504 PRO 3.1 12.9 + - - -
514 LYS* 2.9 21.8 + - - -
534 THR* 1.3 77.3 - - - +
554 VAL* 1.3 62.8 + - - +
574 GLU* 3.4 10.0 + - - +
584 ASN* 3.2 28.4 + - - +
50Y PRO 5.3 1.1 - - - -
54Y SER* 3.3 35.7 - - - -
58Y ASN* 5.3 5.1 + - - -
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Residues in contact with VAL 55 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514 LYS 3.4 18.2 - - - +
524 PHE* 3.1 12.5 + - - +
544 SER* 1.3 83.7 + - - +
564 ASN* 1.3 58.3 + - - +
584 ASN* 3.3 3.9 + - - +
594 VAL* 2.8 53.4 + - + +
774 GLN* 5.4 0.7 - - - +
804 GLY* 4.5 8.3 - - - +
814 LEU* 4.5 12.3 - - + +
844 ALA* 4.2 18.4 - - + -
1244 ILE* 6.1 1.1 - - - -
1254 ILE* 4.0 25.6 - - + -
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Residues in contact with ASN 56 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133 ARG* 4.3 14.3 - - - +
524 PHE 3.0 16.8 + - - -
534 THR* 3.1 14.9 + - + +
554 VAL* 1.3 76.8 - - - +
574 GLU* 1.3 56.3 + - - +
604 SER* 2.9 33.8 + - - -
774 GLN* 3.4 20.4 + - - +
814 LEU* 3.4 30.3 - - - +
207 T 5.2 4.9 + - - +
217 A 4.4 30.5 + - - +
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Residues in contact with GLU 57 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534 THR* 3.1 12.6 + - + +
544 SER* 3.7 12.1 - - - +
554 VAL 3.2 0.2 - - - -
564 ASN* 1.3 77.2 - - - +
584 ASN* 1.3 70.5 + - - +
604 SER* 3.6 3.6 - - - -
614 ALA* 3.1 22.7 + - + +
51Y LYS* 4.2 31.6 - - - +
87Y LEU* 5.8 3.5 - - - +
88Y ASN* 5.2 4.2 - - - +
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Residues in contact with ASN 58 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544 SER* 3.2 16.4 + - - +
554 VAL* 4.0 2.4 - - - +
574 GLU* 1.3 85.5 - - - +
594 VAL* 1.3 66.2 + - - +
614 ALA* 3.2 10.0 + - - +
624 VAL* 3.1 26.1 + - - +
1244 ILE* 3.6 27.4 - - + +
54Y SER* 5.5 4.8 + - - -
55Y VAL* 6.4 0.2 - - - +
58Y ASN* 4.2 18.0 - - - +
124Y ILE* 4.3 9.6 + - - +
125Y ILE* 4.2 17.2 + - - +
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Residues in contact with VAL 59 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554 VAL* 2.8 42.4 + - + +
584 ASN* 1.3 71.0 - - - +
604 SER* 1.3 64.2 + - - +
624 VAL* 3.1 9.7 + - - +
634 LEU* 3.0 30.3 + - + +
764 TYR 4.4 6.7 - - - +
774 GLN* 3.3 28.0 - - - +
804 GLY* 5.0 1.6 - - - -
1214 VAL* 4.1 37.9 - - + +
1244 ILE* 4.9 8.1 - - + -
1254 ILE* 4.6 6.1 - - + -
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Residues in contact with SER 60 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892 ARG 4.5 4.2 + - - -
902 ILE 4.9 2.0 + - - -
564 ASN 2.9 20.3 + - - -
574 GLU* 3.6 5.4 - - - -
594 VAL* 1.3 77.5 - - - +
614 ALA* 1.3 62.5 + - - +
634 LEU* 3.1 3.8 + - - -
644 THR* 3.0 9.9 + - - -
734 ARG* 2.7 41.9 + - - +
774 GLN* 3.5 9.1 - - - +
217 A 4.8 1.3 - - - -
227 T 2.9 19.5 + - - -
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Residues in contact with ALA 61 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
902 ILE 5.8 0.4 - - - -
574 GLU* 3.1 13.9 + - + +
584 ASN* 3.2 13.2 + - - +
604 SER* 1.3 76.9 - - - +
624 VAL* 1.3 61.6 + - + +
644 THR* 3.2 10.2 + - - -
654 GLN* 3.1 26.2 + - + +
126Y THR 5.9 2.7 - - - +
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Residues in contact with VAL 62 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584 ASN 3.1 15.0 + - - +
594 VAL* 3.3 9.9 - - + +
614 ALA* 1.3 76.6 - - + +
634 LEU* 1.3 61.7 + - + +
654 GLN* 2.9 11.9 + - + +
664 TYR* 2.9 51.5 + - + -
1174 VAL* 5.5 0.7 - - + +
1204 ALA* 3.8 17.7 - - + -
1214 VAL* 5.0 4.3 - - + +
1244 ILE* 3.7 32.1 - - + -
126Y THR 5.0 8.1 - - - +
127Y GLY* 5.1 1.3 - - - -
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Residues in contact with LEU 63 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594 VAL* 3.0 33.0 + - + +
604 SER* 3.1 7.8 + - - +
624 VAL* 1.3 77.1 - - + +
644 THR* 1.3 61.1 + - - +
664 TYR* 3.2 3.3 + - - +
674 GLY 3.0 4.5 + - - -
684 ILE* 2.9 38.6 + - + +
734 ARG* 3.5 47.8 - - + +
764 TYR* 3.6 32.5 - - + -
774 GLN* 4.0 10.5 - - - +
1174 VAL* 3.6 18.8 - - + -
1214 VAL* 5.0 3.6 - - + -
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Residues in contact with THR 64 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
902 ILE* 2.6 27.4 + - + +
912 GLY* 3.6 14.6 - - - +
922 SER 3.4 28.0 - - - +
932 GLY* 4.5 1.6 - - - -
942 PRO* 3.3 3.7 - - + +
952 ALA* 3.2 19.4 + - + +
604 SER 3.0 4.8 + - - -
614 ALA* 3.4 11.4 - - - -
624 VAL 3.1 0.4 - - - -
634 LEU* 1.3 76.8 - - - +
654 GLN* 1.3 63.1 + - - +
674 GLY 3.1 10.2 + - - -
734 ARG* 2.9 23.9 + - - +
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Residues in contact with GLN 65 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
922 SER 4.9 7.9 + - - -
932 GLY* 5.3 0.8 - - - -
942 PRO* 3.4 32.1 - - - +
614 ALA* 3.1 17.7 + - + +
624 VAL* 2.9 12.1 + - + +
644 THR* 1.3 77.7 - - - +
664 TYR* 1.3 62.2 + - + +
674 GLY 3.3 0.4 - - - -
92Y SER* 4.4 17.6 + - - -
126Y THR 6.0 0.9 - - - +
133Y VAL* 3.9 20.1 - - - +
134Y SER* 3.0 42.0 + - - +
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Residues in contact with TYR 66 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
942 PRO* 4.7 0.9 - - - -
624 VAL* 2.9 35.0 + - + +
634 LEU* 3.2 6.2 + - - +
654 GLN* 1.3 80.4 - - + +
674 GLY* 1.3 61.9 + - - +
684 ILE* 3.2 20.7 + - + +
1164 GLN* 3.2 42.0 + - + -
1174 VAL* 3.9 19.5 - - + -
1204 ALA* 3.5 30.5 - - + +
134Y SER* 5.9 5.6 - - - -
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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
------------------------------------------------------------
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