Contacts of the strand formed by residues 75 - 89 (chain H) in PDB entry 5IXM
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 ALA 75 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125G THR* 3.0 25.3 + - - +
66H THR* 3.8 28.5 - - + +
68H SER 3.9 4.3 - - - -
69H ILE* 4.4 0.7 - - - -
70H PHE* 3.6 10.1 - - - -
73H GLY 3.8 0.6 + - - -
74H VAL* 1.3 78.3 - - - +
76H ALA* 1.3 60.8 + - - +
78H ASN* 4.2 8.7 - - - +
108H ASP* 4.2 25.9 - - + +
110H PRO* 6.2 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 76 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454G ILE* 3.7 17.9 - - + -
68H SER* 2.7 30.0 + - - +
69H ILE* 3.9 2.2 - - - -
70H PHE* 3.5 31.6 - - + -
74H VAL 3.5 0.4 + - - -
75H ALA* 1.3 73.0 - - - +
77H GLU* 1.3 63.1 + - + +
107H PHE* 3.3 12.0 - - + -
108H ASP* 3.0 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 77 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411G LEU* 3.8 14.4 - - - +
431G ARG* 2.5 46.3 + - - +
432G TYR 4.7 3.3 + - - +
433G ALA* 4.4 2.9 - - - +
454G ILE* 4.4 8.0 - - - +
66H THR* 3.7 3.3 - - - +
67H VAL* 3.0 33.6 + - + -
68H SER* 2.9 19.4 + - - +
76H ALA* 1.3 78.5 - - + +
78H ASN* 1.3 65.9 + - - +
105H THR* 3.9 12.8 - - + +
106H PHE 3.6 3.6 - - - -
107H PHE* 3.5 39.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 78 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64H GLN* 4.2 19.4 - - + +
65H GLU 3.6 5.6 - - - +
66H THR* 3.0 30.8 + - - +
67H VAL* 4.4 2.7 - - - -
75H ALA* 4.2 4.0 - - - +
77H GLU* 1.3 76.5 - - - +
79H GLN* 1.3 60.4 + - - +
105H THR* 3.2 5.9 - - - +
106H PHE* 2.9 54.7 + - + +
108H ASP* 3.3 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 79 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397G LYS* 5.6 1.4 + - - -
431G ARG* 5.2 4.7 + - - -
553G GLN* 2.8 39.6 + - - +
63H SER 3.9 0.3 - - - +
64H GLN* 3.4 5.6 - - - -
65H GLU 2.9 30.9 + - - +
67H VAL* 3.6 24.4 - - + +
78H ASN* 1.3 74.1 - - - +
80H LEU* 1.3 71.0 + - - +
81H VAL* 4.0 2.1 + - + +
103H PHE* 3.8 30.8 - - + +
104H ARG 3.2 15.3 - - - +
105H THR* 4.1 11.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63H SER 3.5 4.0 - - - +
64H GLN* 3.5 41.5 - - + +
79H GLN* 1.3 73.4 - - - +
81H VAL* 1.3 61.9 + - - +
103H PHE* 3.3 5.7 - - - -
104H ARG* 2.9 33.0 + - + +
106H PHE* 3.7 20.4 - - + -
120H ALA* 4.0 15.3 - - + +
123H LEU* 3.8 36.6 - - + -
124H ARG* 4.2 22.9 - - + +
127H MET* 3.4 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 81 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553G GLN* 3.6 26.9 - - + +
61H SER 3.8 0.2 - - - +
62H GLU* 3.3 7.6 - - - +
63H SER* 3.0 39.2 + - - +
79H GLN* 4.0 8.7 - - + +
80H LEU* 1.3 79.6 - - - +
82H LEU* 1.3 64.2 + - - +
83H HIS* 3.4 34.3 - - + +
101H ASN* 5.4 0.2 - - + -
102H VAL 3.4 5.2 - - - +
103H PHE* 3.5 36.6 - - + -
127H MET* 3.6 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H LEU* 4.9 2.0 - - + -
60H SER* 4.2 9.9 - - - +
61H SER 3.5 16.2 - - - +
62H GLU* 4.1 18.6 - - + +
81H VAL* 1.3 75.1 - - - +
83H HIS* 1.3 68.7 + - - +
84H VAL* 4.0 14.6 - - + -
100H VAL 3.6 1.2 - - - +
101H ASN* 3.3 6.1 - - - +
102H VAL* 2.9 36.8 + - + +
127H MET* 3.3 22.6 - - + +
128H ARG* 3.8 44.9 - - + +
131H ALA* 4.1 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 83 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554G SER* 5.2 10.3 - - - -
60H SER* 3.2 5.9 - - - -
61H SER* 2.9 55.0 + - - +
63H SER* 4.0 17.8 + - - -
81H VAL* 3.4 29.4 - - + +
82H LEU* 1.3 74.1 - - - +
84H VAL* 1.3 62.2 + - - +
85H GLN 4.3 0.4 - - - -
99H GLN* 5.1 8.8 + - - +
100H VAL 3.6 3.1 - - - -
101H ASN* 2.9 25.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 84 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H LEU* 3.9 30.5 - - + -
57H ILE* 4.9 7.2 - - + -
59H GLY 3.8 7.6 - - - +
60H SER* 4.0 2.0 - - - -
82H LEU* 4.0 21.8 - - + -
83H HIS* 1.3 80.1 - - - +
85H GLN* 1.3 68.1 - - - +
86H ALA* 4.1 1.9 + - + +
99H GLN* 3.4 10.1 - - - +
100H VAL* 2.9 45.8 + - + +
101H ASN* 4.5 0.4 + - - -
131H ALA* 4.4 12.6 - - + -
135H LEU* 4.5 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 85 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57H ILE* 3.9 2.4 - - - +
58H ILE* 2.9 45.7 + - + +
59H GLY 3.3 14.9 + - - +
83H HIS 4.3 0.4 - - - -
84H VAL* 1.3 73.6 - - - +
86H ALA* 1.3 64.5 + - - +
87H GLN* 6.0 0.7 - - + +
97H PRO* 4.6 7.1 - - - +
98H LEU 2.6 29.3 + - - +
99H GLN* 3.2 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 86 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H LEU* 4.5 11.0 - - + -
56H ARG 3.3 11.4 - - - +
57H ILE* 4.5 7.2 - - + -
58H ILE* 3.5 1.9 - - - +
84H VAL* 4.1 2.6 + - + -
85H GLN* 1.3 79.2 - - - +
87H GLN* 1.3 71.4 + - - +
97H PRO* 3.6 0.9 - - - +
98H LEU* 2.9 40.6 + - + +
135H LEU* 4.2 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 87 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H THR 3.7 0.5 - - - +
55H LEU* 3.5 5.6 - - - +
56H ARG* 2.9 66.4 + - + +
58H ILE* 3.5 20.1 - - + +
85H GLN* 6.0 0.6 - - + +
86H ALA* 1.3 84.7 - - - +
88H VAL* 1.3 63.6 + - - +
89H LEU* 4.1 4.6 - - + +
95H ILE* 3.6 27.5 - - + +
96H TYR 3.7 4.9 - - - -
97H PRO* 4.1 15.7 - - + +
98H LEU* 4.5 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 88 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H LEU* 4.7 10.3 - - + -
17H LEU* 6.6 0.2 - - + -
53H PRO* 5.1 3.1 - - + -
54H THR 3.4 8.3 - - - +
55H LEU* 3.9 14.4 - - + -
87H GLN* 1.3 75.5 - - - +
89H LEU* 1.3 62.5 + - - +
90H ILE* 3.9 17.2 + - + -
95H ILE* 3.5 3.3 - - - +
96H TYR* 2.9 41.9 + - + +
98H LEU* 3.8 27.4 - - + -
139H LEU* 4.6 8.5 - - + -
142H VAL* 4.0 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H GLU* 5.9 0.2 - - - +
53H PRO* 3.2 4.9 - - - +
54H THR* 2.9 63.8 + - + +
56H ARG* 3.5 42.0 - - + +
87H GLN* 4.1 10.8 - - + +
88H VAL* 1.3 71.6 - - - +
90H ILE* 1.3 62.1 + - - +
91H PRO* 3.8 2.1 - - - +
95H ILE* 3.6 29.4 - - + +
----------------------------------------------------------
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