Contacts of the strand formed by residues 90 - 101 (chain d) in PDB entry 4PJO
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 90 (chain d).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75d THR* 3.3 5.5 + - - -
76d GLU* 2.8 56.9 + - + +
77d VAL 3.7 17.9 - - - +
88d LYS 3.3 4.1 + - - +
89d PRO* 1.3 71.5 - - - +
91d ASN* 1.3 77.1 + - - +
92d LYS* 4.4 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 91 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74d TRP 3.8 6.6 - - - +
75d THR* 3.8 11.6 + - - -
89d PRO 4.1 4.1 + - - +
90d VAL* 1.3 84.3 - - - +
92d LYS* 1.3 70.5 - - - +
93d ASP* 6.1 0.4 - - - +
44k TYR* 5.5 2.7 + - - -
46k ARG* 5.8 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 92 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73d MET* 3.3 3.6 - - - +
74d TRP* 3.0 59.9 + - + +
76d GLU* 3.6 44.5 + - + +
90d VAL* 4.4 14.6 - - + +
91d ASN* 1.3 84.8 - - - +
93d ASP* 1.3 68.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 93 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71d LYS* 4.1 30.8 + - - -
72d GLU 3.1 13.5 - - - +
73d MET* 4.2 4.3 - - + -
74d TRP* 3.8 6.4 - - - -
91d ASN* 6.1 0.3 - - - +
92d LYS* 1.3 80.3 - - - +
94d ARG* 1.3 66.7 + - - +
95d TYR* 4.7 11.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 94 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1362 G 5.6 0.2 - - - +
16c THR* 6.2 0.2 - - - +
18c GLU* 2.7 30.9 + - - -
24c GLN* 4.9 7.4 + - - +
67c TYR* 3.3 11.9 + - - -
69c ILE* 3.8 18.2 - - - +
50d LYS* 5.3 2.2 - - - +
71d LYS* 3.4 3.4 - - - -
72d GLU* 2.6 60.6 + - + +
74d TRP* 4.1 11.6 - - + -
93d ASP* 1.3 81.2 - - - +
95d TYR* 1.3 66.8 + - - +
96d ILE* 3.7 21.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 95 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69d ASN 6.0 0.9 - - - -
70d VAL 3.5 10.8 - - - +
71d LYS* 3.8 39.5 + - + -
93d ASP* 4.7 9.8 + - - -
94d ARG* 1.3 79.5 - - - +
96d ILE* 1.3 64.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 96 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67c TYR* 4.6 0.7 - - + -
69c ILE* 3.8 35.7 - - + -
69d ASN* 3.8 0.3 - - - -
70d VAL* 2.8 40.2 + - + +
72d GLU* 4.2 13.2 - - + +
94d ARG* 3.7 42.4 - - + +
95d TYR* 1.3 77.3 - - - +
97d SER* 1.3 62.5 + - - +
98d LYS 4.2 4.9 - - - +
99d MET* 4.0 39.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 97 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69c ILE* 5.9 0.2 - - - +
72c ASP* 3.0 40.2 + - - -
67d LEU 5.2 0.2 - - - -
68d GLU* 3.2 7.0 - - - +
69d ASN* 3.0 33.8 + - - +
96d ILE* 1.3 75.6 - - - +
98d LYS* 1.3 73.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 98 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69c ILE* 3.8 1.2 - - - +
70c LEU* 2.8 48.8 + - + +
71c PRO 3.8 6.5 - - - +
72c ASP 2.9 26.3 + - - +
73c SER* 3.6 3.8 + - - +
74c LEU* 2.7 30.5 + - + +
75c PRO* 5.0 0.6 - - - +
76c LEU* 3.7 32.3 - - + +
67d LEU 3.4 6.1 - - - +
68d GLU* 4.0 14.8 - - + -
96d ILE* 4.2 4.2 - - - +
97d SER* 1.3 94.4 + - - +
99d MET* 1.3 62.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 99 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67c TYR* 3.4 54.5 - - + -
68c PHE 3.3 11.9 - - - +
69c ILE* 4.5 0.4 - - + -
70c LEU* 4.0 5.9 - - - +
52d LEU* 4.4 9.6 - - + -
66d VAL* 3.4 9.4 - - - +
67d LEU* 2.8 57.5 + - + +
70d VAL* 3.8 32.3 - - + +
96d ILE* 4.0 22.4 - - + -
97d SER 4.4 0.2 - - - -
98d LYS* 1.3 74.9 - - - +
100d PHE* 1.3 62.9 + - - +
101d LEU* 5.3 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 100 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1312 U 5.4 0.2 - - - -
3c LEU* 3.7 38.1 - - + -
4c VAL 4.8 0.7 - - - -
6c PHE* 4.2 3.4 - + - -
7c LEU* 3.7 41.1 - - + -
36c MET* 4.0 14.8 - - + -
67c TYR* 3.1 6.0 - - - +
68c PHE* 2.9 46.6 + + + -
70c LEU* 4.1 7.4 - - + +
64d ASN* 3.7 28.7 - - + -
65d MET 3.3 5.4 - - - -
66d VAL* 3.8 17.9 - - + +
99d MET* 1.3 74.2 - - - +
101d LEU* 1.3 75.1 + - - +
102d ARG* 4.0 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66c ARG 3.4 13.0 - - - +
67c TYR* 4.0 17.9 - - + -
44d ILE* 4.3 17.0 - - + -
46d CYS* 4.3 17.9 - - - -
52d LEU* 3.9 23.1 - - + -
63d CYS 5.1 1.1 - - - +
64d ASN* 3.3 3.3 - - - -
65d MET* 2.8 37.1 + - + +
67d LEU* 4.5 12.3 - - + -
99d MET* 4.1 3.0 - - + +
100d PHE* 1.3 76.6 - - - +
102d ARG* 1.3 83.6 + - - +
105d SER* 4.3 4.3 - - - -
106d VAL* 4.1 22.2 - - + -
----------------------------------------------------------
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