Contacts of the strand formed by residues 110 - 118 (chain B) in PDB entry 1SNF
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 ARG 110 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B SER* 5.3 10.3 + - - -
20B ALA* 5.3 10.3 - - - +
28B ASP* 2.9 41.2 + - + +
29B LEU 3.4 7.4 - - - +
30B TYR* 3.4 40.2 + - + -
64B ARG* 3.4 39.8 + - - +
67B LEU* 3.5 13.7 - - - +
108B GLY 3.8 0.6 + - - -
109B ASP* 1.3 73.6 - - - +
111B ILE* 1.3 60.2 + - - +
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Residues in contact with ILE 111 (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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29B LEU 2.8 20.3 + - - +
30B TYR 4.0 10.3 - - - +
31B SER* 3.9 9.9 - - - -
45B VAL* 4.0 25.1 - - + -
47B THR* 4.4 3.4 - - + -
63B PRO* 5.2 0.3 - - - +
64B ARG* 3.9 11.0 + - - +
67B LEU* 4.8 4.0 - - + -
73B LEU* 4.4 9.2 - - + +
75B ILE* 4.6 2.4 - - - +
92B VAL* 4.0 26.9 - - + -
94B LEU* 3.8 31.2 - - + +
105B VAL* 3.9 28.5 - - + -
109B ASP* 3.6 12.1 - - + +
110B ARG* 1.3 78.0 - - - +
112B ALA* 1.3 61.6 + - + +
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Residues in contact with ALA 112 (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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28B ASP* 3.5 9.4 - - - +
29B LEU* 3.0 29.8 + - + +
61B VAL* 3.8 21.8 - - + -
62B HIS 3.4 15.3 - - - +
64B ARG* 3.8 12.9 - - - +
75B ILE* 4.0 7.6 - - + -
92B VAL* 4.3 13.2 - - + -
111B ILE* 1.3 78.3 - - + +
113B GLN* 1.3 61.9 + - - +
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Residues in contact with GLN 113 (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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26B GLY* 4.0 18.5 + - - -
27B VAL 3.2 10.8 - - - +
28B ASP* 3.6 15.8 - - - +
29B LEU* 4.4 2.9 - - - +
60B LEU 3.6 1.0 - - - +
61B VAL* 3.6 3.4 - - - -
62B HIS* 2.9 44.8 + - + +
63B PRO 3.3 20.1 + - - +
64B ARG* 4.4 3.4 - - + +
65B SER* 4.9 1.2 - - - +
112B ALA* 1.3 79.0 - - - +
114B LEU* 1.3 59.1 + - - +
115B LEU* 4.2 4.2 - - + +
81C THR* 3.7 35.5 + - - +
83C ASP* 4.9 4.9 - - - +
3170C UMP 3.8 20.1 + - - -
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Residues in contact with LEU 114 (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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5B LEU* 4.4 22.7 - - + -
7B ILE* 6.2 0.9 - - + -
19B ARG* 5.1 0.9 + - - -
25B ALA 4.3 0.3 - - - +
26B GLY* 3.2 1.6 - - - -
27B VAL* 2.9 47.8 + - + +
29B LEU* 4.1 16.6 - - + +
51B VAL* 4.4 10.8 - - + -
53B VAL* 6.0 0.4 - - + -
59B GLY* 4.1 7.6 - - - -
60B LEU 3.3 30.5 - - - +
61B VAL* 4.1 13.5 - - + +
82B ILE* 4.3 7.9 - - + -
90B ILE* 4.3 19.7 - - + -
113B GLN* 1.3 73.2 - - - +
115B LEU* 1.3 67.2 - - - +
116B VAL* 4.9 3.6 - - + +
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Residues in contact with LEU 115 (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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25B ALA* 3.6 35.4 - - + +
26B GLY* 4.0 9.2 - - - -
59B GLY* 3.3 5.4 - - - -
60B LEU* 2.8 44.0 + - + +
62B HIS* 3.5 45.1 - - + +
113B GLN* 4.2 15.9 - - + +
114B LEU* 1.3 77.9 - - - +
116B VAL* 1.3 67.8 + - - +
117B GLN* 5.0 5.8 - - + -
3174B TRS 4.2 7.9 - - - +
58C VAL* 4.6 11.0 - - + -
60C LEU* 4.9 0.2 - - + -
81C THR* 4.6 5.6 - - + -
119C VAL* 4.6 8.7 - - + -
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Residues in contact with VAL 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LEU* 4.4 19.5 - - + -
25B ALA 4.7 0.8 + - - -
53B VAL* 4.5 7.9 - - + -
54B PRO* 4.8 2.9 - - + -
57B MET* 3.8 33.2 - - + -
58B VAL 3.3 12.1 - - - +
59B GLY* 4.7 4.7 - - - -
114B LEU* 4.9 6.1 - - + +
115B LEU* 1.3 79.4 - - - +
117B GLN* 1.3 69.1 + - - +
119C VAL* 3.5 5.0 - - - +
120C GLU* 3.0 31.8 + - + +
122C VAL* 4.0 33.8 - - + +
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Residues in contact with GLN 117 (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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117A GLN* 3.0 21.7 + - - +
57B MET* 3.0 7.8 - - - +
58B VAL* 2.8 40.1 + - + +
60B LEU* 3.0 11.8 - - + +
115B LEU* 4.3 5.8 - - + -
116B VAL* 1.3 80.8 - - - +
118B ARG* 1.3 62.3 + - - +
3174B TRS 2.9 28.9 + - - -
58C VAL* 4.1 11.9 - - - +
117C GLN* 3.1 26.6 + - - +
118C ARG 3.0 28.0 + - - +
119C VAL* 4.4 6.3 - - + +
120C GLU* 4.4 5.6 - - - +
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Residues in contact with ARG 118 (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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117A GLN* 3.1 26.9 + - - +
118A ARG 5.6 0.3 + - - -
56B GLY* 3.4 14.2 + - - +
57B MET* 4.0 21.2 - - + +
117B GLN* 1.3 74.8 - - - +
119B VAL* 1.3 59.5 + - - +
120B GLU* 6.1 0.9 - - - +
120C GLU* 3.0 31.8 + - - +
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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