Contacts of the strand formed by residues 95 - 107 (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 ILE 95 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56B ARG* 5.4 3.4 - - - +
87B GLN* 4.1 26.7 - - + +
88B VAL 3.5 12.8 - - - +
89B LEU* 4.1 38.6 - - + +
94B ASP* 1.3 84.2 - - + +
96B TYR* 1.3 64.3 + - - +
97B PRO* 3.5 10.7 - - + +
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Residues in contact with TYR 96 (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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347A VAL* 6.1 0.7 - - - +
87B GLN 3.8 0.2 - - - -
88B VAL* 2.9 39.3 + - - +
93B HIS* 6.5 0.7 - - + -
94B ASP 3.8 3.5 + - - +
95B ILE* 1.3 75.0 - - - +
97B PRO* 1.3 81.2 - - + +
98B LEU* 3.7 14.2 + - + +
141B THR* 4.0 25.6 + - - -
142B VAL* 3.6 37.9 - - + +
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Residues in contact with PRO 97 (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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86B ALA 3.7 9.0 - - - +
87B GLN* 4.4 11.2 - - + +
95B ILE* 3.5 10.5 - - + +
96B TYR* 1.3 102.4 - - + +
98B LEU* 1.3 68.5 + - - +
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Residues in contact with LEU 98 (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* 4.8 3.1 - - + -
85B GLN* 3.7 3.5 - - - +
86B ALA* 2.9 45.8 + - + +
88B VAL* 3.7 24.0 - - + -
96B TYR* 3.7 29.2 - - + +
97B PRO* 1.3 83.4 - - - +
99B GLN* 1.3 62.0 + - - +
135B LEU* 4.0 27.4 - - + +
138B GLN* 3.4 31.0 - - + +
139B LEU* 4.9 2.5 - - + -
141B THR* 4.1 2.9 - - - +
142B VAL* 3.9 10.1 - - + -
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Residues in contact with GLN 99 (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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83B HIS* 5.2 7.7 + - - +
84B VAL 3.4 10.3 - - - +
85B GLN* 3.7 29.9 - - + +
98B LEU* 1.3 77.4 - - - +
100B VAL* 1.3 71.6 + - - +
101B ASN* 4.3 24.5 + - - +
138B GLN* 3.4 14.8 + - - +
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Residues in contact with VAL 100 (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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82B LEU 3.4 2.3 - - - +
84B VAL* 2.9 42.9 + - + +
99B GLN* 1.3 80.9 - - - +
101B ASN* 1.3 69.6 + - - +
102B VAL* 4.0 7.4 - - + -
131B ALA* 3.9 24.7 - - + -
134B GLN* 3.3 32.1 - - + +
135B LEU* 3.9 30.5 - - + -
138B GLN* 3.6 17.9 - - - +
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Residues in contact with ASN 101 (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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554A SER 5.7 0.4 + - - -
556A PHE 2.7 33.0 + - - +
81B VAL* 5.3 0.2 - - + -
82B LEU 3.2 3.8 - - - +
83B HIS* 2.6 36.9 + - + +
99B GLN* 4.3 19.4 + - - +
100B VAL* 1.3 83.9 - - - +
102B VAL* 1.3 65.1 + - - +
103B PHE* 3.9 20.1 - - + -
134B GLN* 4.4 10.5 + - - +
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Residues in contact with VAL 102 (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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81B VAL* 3.4 4.5 - - - +
82B LEU* 2.9 37.1 + - + +
100B VAL* 4.0 18.8 - - + -
101B ASN* 1.3 78.8 - - - +
103B PHE* 1.3 66.6 + - - +
104B ARG* 3.6 11.0 - - - +
127B MET* 3.2 30.2 - - + +
130B GLN* 3.6 27.4 - - + +
131B ALA* 4.0 23.1 - - + +
134B GLN* 4.1 10.1 - - - +
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Residues in contact with PHE 103 (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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397A LYS* 3.4 31.0 - - - +
553A GLN* 5.7 2.5 - - + -
554A SER 3.8 23.3 - - - -
555A ALA* 4.2 4.3 - - - -
556A PHE* 4.0 22.0 - - - -
79B GLN* 3.8 26.0 - - - +
80B LEU 3.4 4.3 - - - +
81B VAL* 3.7 35.9 - - + -
83B HIS* 5.4 0.7 - + - -
101B ASN* 3.9 28.9 - - + -
102B VAL* 1.3 78.7 - - - +
104B ARG* 1.3 82.6 + - - +
127B MET* 4.5 0.4 - - - -
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Residues in contact with ARG 104 (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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311A ASP* 4.1 24.4 + - - -
313A SER* 3.6 25.0 + - - -
79B GLN* 3.2 8.9 - - - +
80B LEU* 2.9 32.9 + - + +
102B VAL* 3.6 10.5 - - - +
103B PHE* 1.3 87.4 + - - +
105B THR* 1.3 62.5 + - - +
123B LEU* 4.4 29.4 - - + +
126B GLU* 3.9 29.2 + - - +
127B MET* 3.5 30.9 - - + +
130B GLN* 2.8 36.5 + - - +
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Residues in contact with THR 105 (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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309A GLN* 3.1 32.1 + - - +
431A ARG* 3.3 34.7 + - - +
67B VAL* 4.9 0.8 - - + +
77B GLU* 3.9 19.1 - - + +
78B ASN 3.3 11.8 + - - +
79B GLN* 4.1 15.9 + - - +
104B ARG* 1.3 79.3 + - - +
106B PHE* 1.3 69.0 + - - +
123B LEU* 4.8 4.2 - - - +
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Residues in contact with PHE 106 (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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309A GLN* 3.3 10.3 - - + +
64B GLN* 4.1 17.0 - - - -
77B GLU* 4.4 2.2 - - - -
78B ASN* 2.9 48.0 + - + +
80B LEU* 3.8 30.7 - - + -
105B THR* 1.3 77.8 - - - +
107B PHE* 1.3 83.7 + - - +
108B ASP* 3.8 7.8 + - - -
116B LYS* 4.1 23.1 - - + -
119B GLU* 3.6 33.0 - - + +
120B ALA* 4.6 12.3 - - + -
123B LEU* 3.6 22.0 - - + -
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Residues in contact with PHE 107 (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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309A GLN* 3.5 14.2 + - - -
411A LEU* 3.7 10.8 - - + -
433A ALA* 3.5 27.1 - - + -
437A TYR* 3.5 28.3 - + - -
438A ILE* 4.1 22.7 - - + -
441A ALA* 5.2 2.2 - - + -
442A VAL* 4.0 33.0 - - + -
454A ILE* 4.4 7.0 - - + -
70B PHE* 4.7 6.5 - + - -
76B ALA* 3.2 26.0 - - + -
77B GLU* 3.6 23.8 - - + -
105B THR* 6.1 0.2 - - + -
106B PHE* 1.3 82.3 - - - +
108B ASP* 1.3 61.2 + - - +
116B LYS* 2.8 26.4 + - - +
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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