Contacts of the strand formed by residues 75 - 89 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A THR* 3.0 25.4 + - - +
66B THR* 3.7 30.7 - - + +
68B SER 3.8 4.5 - - - -
69B ILE* 4.3 0.7 - - - -
70B PHE* 3.9 4.6 - - - -
74B VAL* 1.3 86.3 - - + +
76B ALA* 1.3 60.6 + - - +
78B ASN* 4.0 16.2 - - - +
108B ASP* 4.4 17.7 - - + +
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Residues in contact with ALA 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A ILE* 3.8 19.7 - - + -
68B SER* 2.7 27.1 + - - +
69B ILE 3.9 2.2 - - - -
70B PHE* 3.6 32.0 - - + -
74B VAL 3.6 0.4 + - - -
75B ALA* 1.3 74.3 - - - +
77B GLU* 1.3 62.3 + - + +
107B PHE* 3.2 11.9 - - + -
108B ASP* 3.1 27.0 + - - +
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Residues in contact with GLU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A LEU* 3.6 15.4 - - - +
431A ARG* 2.4 47.3 + - - +
432A TYR 4.6 2.9 - - - +
433A ALA* 4.3 2.8 - - - +
454A ILE* 4.5 6.9 - - - +
66B THR* 3.8 2.8 - - - +
67B VAL* 3.0 32.1 + - + -
68B SER* 3.0 20.7 + - - +
76B ALA* 1.3 78.3 - - + +
78B ASN* 1.3 66.7 + - - +
105B THR* 3.9 12.7 - - + +
106B PHE 3.7 3.4 - - - -
107B PHE* 3.6 39.0 - - + -
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Residues in contact with ASN 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLN* 4.3 19.2 - - + +
65B GLU 3.6 5.8 - - - +
66B THR* 3.1 31.5 + - - +
67B VAL* 4.5 2.2 - - - -
75B ALA* 4.0 5.9 - - - +
77B GLU* 1.3 75.2 - - - +
79B GLN* 1.3 62.0 + - - +
105B THR* 3.3 4.9 - - - +
106B PHE* 2.9 52.6 + - + +
108B ASP* 3.3 40.8 + - - +
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Residues in contact with GLN 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A LYS* 5.6 1.6 + - - -
431A ARG* 5.2 5.2 + - - -
553A GLN* 2.6 36.0 + - - +
63B SER 3.8 0.3 - - - +
64B GLN* 3.3 5.8 - - - +
65B GLU 3.0 28.7 + - - +
67B VAL* 3.7 24.5 - - + +
78B ASN* 1.3 74.0 - - - +
80B LEU* 1.3 71.0 + - - +
81B VAL* 4.0 4.7 + - + +
103B PHE* 3.8 31.5 - - + +
104B ARG 3.2 15.5 - - - +
105B THR* 4.1 12.7 + - - +
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Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B SER 3.4 3.6 - - - +
64B GLN* 3.5 41.3 - - + +
79B GLN* 1.3 73.2 - - - +
81B VAL* 1.3 62.0 + - - +
103B PHE* 3.4 5.4 - - - -
104B ARG* 2.9 34.1 + - + +
106B PHE* 3.8 27.1 - - + -
120B ALA* 4.1 15.7 - - + +
123B LEU* 4.0 28.9 - - + -
124B ARG* 4.3 21.3 - - + +
127B MET* 3.5 15.9 - - + +
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Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A GLN* 3.4 33.9 - - + +
61B SER 3.8 0.3 - - - +
62B GLU* 3.3 7.3 - - - +
63B SER* 2.9 39.6 + - - +
79B GLN* 4.0 3.6 - - + +
80B LEU* 1.3 80.5 - - - +
82B LEU* 1.3 65.3 + - - +
83B HIS* 3.3 34.5 - - + +
101B ASN* 5.3 0.2 - - + -
102B VAL 3.4 4.5 - - - +
103B PHE* 3.7 35.0 - - + -
127B MET* 3.6 2.5 - - - -
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Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 5.1 2.7 - - + -
60B SER* 4.3 8.7 - - - +
61B SER 3.5 18.6 - - - +
62B GLU* 4.2 14.8 - - + +
81B VAL* 1.3 73.6 - - - +
83B HIS* 1.3 70.8 + - - +
84B VAL* 4.0 13.7 - - + -
100B VAL 3.4 1.4 - - - +
101B ASN* 3.2 6.9 - - - +
102B VAL* 2.9 40.1 + - + +
127B MET* 3.4 20.6 - - + +
128B ARG* 3.9 38.6 - - + +
131B ALA* 3.9 19.5 - - + -
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Residues in contact with HIS 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A SER* 5.4 8.3 - - - -
60B SER* 3.2 8.7 - - - -
61B SER* 3.0 54.2 + - - +
63B SER* 4.0 16.6 + - - -
81B VAL* 3.3 28.5 - - + +
82B LEU* 1.3 72.3 - - - +
84B VAL* 1.3 62.6 + - - +
85B GLN* 4.3 2.5 - - + -
99B GLN* 5.2 9.6 + - - +
100B VAL 3.5 3.1 - - - -
101B ASN* 2.6 29.3 + - + +
103B PHE* 5.4 0.2 - + - -
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Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 3.8 29.8 - - + -
57B ILE* 4.8 7.4 - - + -
59B GLY 3.8 8.3 - - - +
60B SER* 4.0 2.0 - - - -
82B LEU* 4.0 22.2 - - + -
83B HIS* 1.3 80.3 - - - +
85B GLN* 1.3 71.1 + - - +
86B ALA* 4.1 1.4 + - + +
99B GLN* 3.4 7.1 - - - +
100B VAL* 2.9 43.0 + - + +
131B ALA* 4.3 11.0 - - + -
135B LEU* 4.1 26.1 - - + +
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Residues in contact with GLN 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ILE* 3.8 3.1 - - - +
58B ILE* 2.9 51.1 + - + +
59B GLY* 3.1 17.1 + - - +
83B HIS* 4.3 3.1 - - + -
84B VAL* 1.3 75.0 - - - +
86B ALA* 1.3 61.5 + - - +
98B LEU 3.7 5.8 - - - +
99B GLN* 3.7 28.6 - - + +
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Residues in contact with ALA 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B LEU* 4.3 11.9 - - + -
56B ARG 3.2 13.0 - - - +
57B ILE* 4.6 4.9 - - + -
58B ILE* 4.4 2.7 - - - +
84B VAL* 4.1 1.9 + - + -
85B GLN* 1.3 73.9 - - - +
87B GLN* 1.3 72.4 + - - +
97B PRO* 3.7 1.9 - - - +
98B LEU* 2.9 36.1 + - + +
135B LEU* 4.0 31.9 - - + -
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Residues in contact with GLN 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B THR 3.6 1.0 - - - +
55B LEU* 3.6 4.9 - - - +
56B ARG* 2.8 71.4 + - + +
58B ILE* 3.3 26.4 - - + +
86B ALA* 1.3 81.8 - - - +
88B VAL* 1.3 63.8 + - - +
89B LEU* 4.0 12.9 - - + +
95B ILE* 4.1 18.2 - - + +
96B TYR 3.8 5.2 - - - -
97B PRO* 4.5 11.2 - - + +
98B LEU 4.5 0.2 - - - +
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Residues in contact with VAL 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B PRO* 5.1 4.5 - - + -
54B THR 3.4 8.7 - - - +
55B LEU* 4.1 8.3 - - + -
87B GLN* 1.3 75.9 - - - +
89B LEU* 1.3 64.4 + - - +
90B ILE* 3.9 18.7 + - + +
94B ASP 4.4 0.7 - - - +
95B ILE* 3.5 3.5 - - - +
96B TYR* 2.9 41.4 + - - +
98B LEU* 3.7 21.8 - - + -
139B LEU* 3.7 28.7 - - + -
142B VAL* 3.5 29.2 - - + -
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Residues in contact with LEU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ILE 4.2 0.7 - - - +
53B PRO* 3.3 4.0 - - - +
54B THR* 2.9 55.8 + - + +
56B ARG* 3.4 42.6 - - + +
87B GLN* 4.0 20.9 - - + +
88B VAL* 1.3 75.2 - - - +
90B ILE* 1.3 61.7 + - - +
91B PRO* 3.8 2.7 - - - +
95B ILE* 4.1 30.5 - - + +
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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