Contacts of the strand formed by residues 75 - 89 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125E THR* 2.9 29.6 + - - +
66F THR* 3.6 28.5 - - + +
68F SER 4.0 4.3 - - - -
69F ILE* 4.1 0.9 - - - -
70F PHE* 3.9 4.0 - - - -
74F VAL* 1.3 81.8 - - - +
76F ALA* 1.3 61.7 + - - +
78F ASN* 4.3 7.6 - - - +
108F ASP* 4.4 24.6 - - + +
110F PRO* 6.1 0.7 - - - +
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Residues in contact with ALA 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454E ILE* 4.0 10.5 - - + -
68F SER* 2.8 29.1 + - - +
69F ILE* 3.8 6.7 - - - -
70F PHE* 3.5 34.0 - - + -
74F VAL 3.6 0.8 + - - -
75F ALA* 1.3 72.7 - - - +
77F GLU* 1.3 64.4 + - + +
107F PHE* 3.3 10.3 - - + -
108F ASP* 3.0 28.6 + - - +
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Residues in contact with GLU 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309E GLN* 5.7 0.3 + - - -
411E LEU* 3.7 14.7 - - - +
431E ARG* 2.5 46.1 + - - +
432E TYR 4.8 2.1 + - - +
433E ALA* 4.3 4.5 - - - +
454E ILE* 4.6 4.9 - - - +
66F THR* 3.6 6.6 - - - +
67F VAL* 2.9 34.1 + - + +
68F SER* 2.9 19.1 + - - +
76F ALA* 1.3 78.8 - - - +
78F ASN* 1.3 63.1 + - - +
105F THR* 4.0 12.5 - - + +
106F PHE 3.6 2.9 - - - -
107F PHE* 3.4 43.8 - - + -
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Residues in contact with ASN 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64F GLN* 3.9 29.6 - - + +
65F GLU 3.4 5.5 - - - +
66F THR* 3.0 30.5 + - - +
67F VAL* 4.5 2.7 - - - -
75F ALA* 4.3 4.5 - - - +
77F GLU* 1.3 76.4 - - - +
79F GLN* 1.3 60.7 + - - +
105F THR* 3.3 5.4 - - - +
106F PHE* 2.9 48.2 + - + +
108F ASP* 3.4 39.4 + - - +
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Residues in contact with GLN 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397E LYS* 5.5 2.4 + - - -
431E ARG* 5.2 4.9 + - - -
553E GLN* 2.7 40.4 + - - +
63F SER 3.7 0.3 - - - +
64F GLN* 3.3 21.7 - - - -
65F GLU 2.9 12.7 + - - +
67F VAL* 3.6 24.7 - - + +
78F ASN* 1.3 74.7 - - - +
80F LEU* 1.3 72.0 + - - +
81F VAL* 3.9 8.5 + - + +
103F PHE* 4.0 23.9 - - + +
104F ARG 3.2 15.7 - - - +
105F THR* 4.1 12.2 + - - +
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Residues in contact with LEU 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F SER 3.3 5.2 - - - +
64F GLN* 3.5 42.2 - - + +
79F GLN* 1.3 72.3 - - - +
81F VAL* 1.3 62.7 + - - +
103F PHE* 3.4 4.0 - - - -
104F ARG* 2.9 33.5 + - + +
106F PHE* 3.5 27.4 - - + -
120F ALA* 4.2 15.7 - - + +
123F LEU* 4.0 28.5 - - + -
124F ARG* 4.2 20.0 - - + +
127F MET* 3.4 17.9 - - + +
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Residues in contact with VAL 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553E GLN* 3.7 26.9 - - + +
61F SER 3.7 0.3 - - - +
62F GLU* 3.3 7.6 - - - +
63F SER* 2.9 40.1 + - - -
79F GLN* 3.9 11.0 - - + +
80F LEU* 1.3 80.1 - - - +
82F LEU* 1.3 64.3 + - - +
83F HIS* 3.3 33.6 - - + +
101F ASN* 5.4 0.2 - - + -
102F VAL 3.4 4.9 - - - +
103F PHE* 3.6 35.2 - - + -
127F MET* 3.6 3.1 - - - -
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Residues in contact with LEU 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F LEU* 5.1 1.3 - - + -
60F SER* 4.2 12.8 - - - -
61F SER 3.4 15.7 - - - +
62F GLU* 4.0 20.4 - - + +
81F VAL* 1.3 72.3 - - - +
83F HIS* 1.3 70.4 + - - +
84F VAL* 4.0 10.5 - - + -
100F VAL 3.5 1.6 - - - +
101F ASN* 3.3 6.8 - - - +
102F VAL* 2.9 38.4 + - + +
127F MET* 3.3 22.9 - - + +
128F ARG* 3.7 44.2 - - + +
131F ALA* 4.1 13.5 - - + -
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Residues in contact with HIS 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554E SER* 5.4 8.3 - - - -
60F SER* 3.1 7.3 - - - -
61F SER* 2.9 55.7 + - - +
63F SER* 3.9 16.9 + - - -
81F VAL* 3.3 30.0 - - + +
82F LEU* 1.3 73.0 - - - +
84F VAL* 1.3 62.4 + - - +
85F GLN* 5.7 2.7 - - + -
99F GLN* 5.4 7.2 + - - +
100F VAL 3.5 3.8 - - - -
101F ASN* 3.0 25.3 + - + +
103F PHE* 5.6 0.4 - + - -
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Residues in contact with VAL 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F LEU* 3.9 30.3 - - + -
57F ILE* 4.9 6.5 - - + -
59F GLY 3.7 7.9 - - - +
60F SER* 4.0 1.8 - - - -
82F LEU* 4.0 20.6 - - + -
83F HIS* 1.3 80.8 - - - +
85F GLN* 1.3 73.0 + - - +
86F ALA* 4.1 1.9 + - + +
99F GLN* 3.3 7.2 - - - +
100F VAL* 2.9 47.0 + - + +
101F ASN* 4.6 0.2 + - - -
131F ALA* 4.3 12.6 - - + -
135F LEU* 4.5 22.0 - - + -
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Residues in contact with GLN 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57F ILE* 3.8 2.8 - - - +
58F ILE* 2.9 53.7 + - + +
59F GLY 3.2 15.3 + - - +
83F HIS* 5.7 2.5 - - + -
84F VAL* 1.3 75.3 - - - +
86F ALA* 1.3 62.2 + - - +
98F LEU 3.7 4.7 - - - +
99F GLN* 3.8 26.9 - - + +
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Residues in contact with ALA 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F LEU* 4.4 10.5 - - + -
56F ARG 3.4 11.2 - - - +
57F ILE* 4.5 7.0 - - + -
58F ILE* 4.3 2.9 - - - +
84F VAL* 4.1 2.8 + - + -
85F GLN* 1.3 74.9 - - - +
87F GLN* 1.3 70.8 + - - +
97F PRO* 3.8 1.4 - - - +
98F LEU* 2.9 44.7 + - + +
135F LEU* 4.4 23.6 - - + -
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Residues in contact with GLN 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F THR 3.8 0.5 - - - +
55F LEU* 3.3 6.4 - - - +
56F ARG* 2.9 62.9 + - + +
58F ILE* 3.5 25.7 - - + +
86F ALA* 1.3 84.3 - - - +
88F VAL* 1.3 64.4 + - - +
89F LEU* 3.9 15.7 - - + +
95F ILE* 4.1 17.2 - - + +
96F TYR 3.7 5.4 - - - -
97F PRO* 4.4 12.2 - - + +
98F LEU 4.5 0.2 - - - +
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Residues in contact with VAL 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F LEU* 6.5 0.9 - - + -
53F PRO* 5.2 4.5 - - + -
54F THR 3.5 7.6 - - - +
55F LEU* 3.9 8.7 - - + -
87F GLN* 1.3 73.2 - - - +
89F LEU* 1.3 64.0 + - - +
90F ILE* 3.8 16.8 + - + +
94F ASP 4.6 0.3 - - - +
95F ILE* 3.7 1.6 - - - +
96F TYR* 2.9 41.6 + - + +
98F LEU* 3.6 22.7 - - + -
139F LEU* 3.6 29.4 - - + -
142F VAL* 3.9 31.0 - - + -
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Residues in contact with LEU 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53F PRO* 3.3 3.6 - - - +
54F THR* 2.9 54.1 + - + +
56F ARG* 3.7 38.8 - - + +
87F GLN* 3.9 29.6 - - + +
88F VAL* 1.3 75.2 - - - +
90F ILE* 1.3 63.4 + - - +
91F PRO* 3.8 2.1 - - - +
95F ILE* 3.4 33.2 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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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