Contacts of the strand formed by residues 95 - 107 (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 ILE 95 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87F GLN* 4.1 30.3 - - + +
88F VAL 3.7 10.1 - - - +
89F LEU* 3.4 46.2 - - + -
90F ILE 4.8 1.1 - - - +
93F HIS 4.8 4.0 - - - +
94F ASP* 1.3 90.7 - - + +
96F TYR* 1.3 64.0 + - - +
97F PRO* 3.5 9.7 - - + +
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Residues in contact with TYR 96 (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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88F VAL* 2.9 43.4 + - + +
94F ASP 3.9 2.1 + - - +
95F ILE* 1.3 74.5 - - - +
97F PRO* 1.3 75.9 - - + +
98F LEU* 3.4 27.8 + - + +
138F GLN 4.7 0.2 - - - -
141F THR* 3.2 29.3 - - + +
142F VAL* 3.5 40.8 - - + -
145F ALA* 4.4 19.1 - - + -
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Residues in contact with PRO 97 (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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86F ALA 3.8 7.6 - - - +
87F GLN* 4.4 11.7 - - + +
95F ILE* 3.5 11.2 - - + +
96F TYR* 1.3 102.6 - - + +
98F LEU* 1.3 68.0 + - - +
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Residues in contact with LEU 98 (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* 4.7 0.4 - - + -
85F GLN* 3.7 4.2 - - - +
86F ALA* 2.9 45.8 + - + +
88F VAL* 3.6 25.6 - - + -
96F TYR* 3.4 38.4 - - + +
97F PRO* 1.3 75.1 - - - +
99F GLN* 1.3 62.9 + - - +
100F VAL* 5.9 1.1 - - + -
135F LEU* 3.9 28.3 - - + +
138F GLN* 3.2 37.5 - - + +
139F LEU* 4.9 3.8 - - + -
141F THR* 6.0 0.2 - - - -
142F VAL* 4.9 1.3 - - + -
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Residues in contact with GLN 99 (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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83F HIS* 5.4 6.7 + - - +
84F VAL 3.3 9.2 - - - +
85F GLN* 3.8 28.0 - - + +
98F LEU* 1.3 76.9 - - - +
100F VAL* 1.3 65.8 + - - +
101F ASN* 4.2 25.0 + - - +
138F GLN* 3.2 23.1 + - - +
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Residues in contact with VAL 100 (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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82F LEU 3.5 2.8 - - - +
84F VAL* 2.9 43.3 + - + +
98F LEU* 5.9 1.1 - - + -
99F GLN* 1.3 82.6 - - - +
101F ASN* 1.3 70.1 + - - +
102F VAL* 3.9 8.7 - - + -
131F ALA* 3.8 29.8 - - + +
134F GLN* 3.4 21.1 - - + +
135F LEU* 4.2 31.9 - - + +
138F GLN* 3.8 16.6 - - - +
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Residues in contact with ASN 101 (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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556E PHE 3.4 27.5 + - - -
82F LEU 3.3 3.8 - - - +
83F HIS* 3.0 31.2 + - + +
99F GLN* 4.2 22.2 + - - +
100F VAL* 1.3 84.1 - - - +
102F VAL* 1.3 65.8 + - - +
103F PHE* 3.9 27.0 - - + -
134F GLN* 4.2 11.1 + - - +
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Residues in contact with VAL 102 (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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81F VAL* 3.4 4.3 - - - +
82F LEU* 2.9 36.7 + - + +
100F VAL* 3.9 9.2 - - + -
101F ASN* 1.3 79.6 - - - +
103F PHE* 1.3 68.8 + - - +
104F ARG* 3.6 7.9 - - - +
127F MET* 3.2 28.5 - - + +
130F GLN* 3.5 30.5 - - + +
131F ALA* 3.9 34.1 - - + +
134F GLN* 4.0 10.5 - - - +
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Residues in contact with PHE 103 (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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397E LYS* 3.6 23.3 - - - +
553E GLN* 5.8 0.9 - - + -
554E SER 3.6 25.4 - - - -
555E ALA* 4.1 3.8 - - - -
556E PHE* 3.8 24.7 - - - -
79F GLN* 4.0 23.1 - - - +
80F LEU 3.4 3.8 - - - +
81F VAL* 3.6 37.9 - - + -
83F HIS* 5.6 0.7 - + - -
101F ASN* 3.9 32.5 - - + -
102F VAL* 1.3 79.0 - - - +
104F ARG* 1.3 86.8 + - - +
127F MET* 4.4 0.7 - - - -
130F GLN* 5.6 0.6 - - - +
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Residues in contact with ARG 104 (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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311E ASP* 4.1 20.9 + - - -
313E SER* 3.5 24.6 + - - -
79F GLN* 3.2 7.3 - - - +
80F LEU* 2.9 33.6 + - + +
102F VAL* 3.6 10.5 - - - +
103F PHE* 1.3 97.4 + - - +
105F THR* 1.3 66.7 + - - +
123F LEU* 4.3 30.3 - - + +
126F GLU* 4.2 25.4 + - - +
127F MET* 3.5 30.7 - - + +
130F GLN* 2.5 38.0 + - - +
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Residues in contact with THR 105 (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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309E GLN* 3.1 33.3 + - - +
431E ARG* 3.2 34.7 + - - +
67F VAL* 4.8 1.2 - - + +
77F GLU* 4.0 19.1 - - + +
78F ASN 3.3 12.2 + - - +
79F GLN* 4.1 15.4 + - - +
104F ARG* 1.3 80.8 + - - +
106F PHE* 1.3 69.7 + - - +
123F LEU* 4.7 4.4 - - - +
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Residues in contact with PHE 106 (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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309E GLN* 3.5 8.7 - - + +
64F GLN* 3.7 22.0 - - - -
77F GLU* 4.4 2.2 - - - -
78F ASN* 2.9 50.9 + - + +
80F LEU* 3.5 36.8 - - + -
105F THR* 1.3 77.1 - - - +
107F PHE* 1.3 84.3 + - - +
108F ASP* 5.0 3.6 - - - -
116F LYS* 4.4 19.7 - - + -
119F GLU* 3.5 32.8 - - + +
120F ALA* 4.7 11.0 - - + -
123F LEU* 3.6 20.9 - - + -
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Residues in contact with PHE 107 (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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309E GLN* 3.9 10.6 + - + +
411E LEU* 3.7 6.1 - - + -
433E ALA* 3.5 21.3 - - + -
437E TYR* 3.4 33.2 - + - -
438E ILE* 3.7 32.1 - - + -
441E ALA* 5.4 4.0 - - + -
442E VAL* 4.7 14.8 - - + -
454E ILE* 4.7 5.2 - - + -
70F PHE* 4.8 4.5 - + - -
76F ALA* 3.3 22.9 - - + -
77F GLU* 3.4 34.5 - - + +
106F PHE* 1.3 82.5 - - - +
108F ASP* 1.3 63.9 + - - +
116F LYS* 3.0 30.0 + - - +
119F GLU* 5.3 0.4 + - - -
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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