Contacts of the strand formed by residues 110 - 118 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A SER* 5.4 5.5 + - - -
20A ALA* 6.0 3.8 - - - +
28A ASP* 3.2 38.7 + - + +
29A LEU 3.3 9.2 - - - +
30A TYR* 3.8 32.6 + - + -
64A ARG* 3.4 44.1 + - - +
67A LEU* 3.6 11.1 - - - +
108A GLY 4.9 0.7 - - - +
109A ASP* 1.3 74.6 - - - +
111A ILE* 1.3 59.3 + - - +
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Residues in contact with ILE 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LEU 2.9 17.9 + - - +
30A TYR 3.8 4.5 - - - +
31A SER* 3.8 28.9 - - - +
45A VAL* 4.1 18.2 - - + -
47A THR* 4.3 5.4 - - + -
63A PRO* 5.1 0.2 - - - +
64A ARG* 4.0 12.4 + - - +
67A LEU* 4.9 5.1 - - + +
73A LEU* 4.8 9.9 - - + +
75A ILE* 4.7 2.9 - - - +
92A VAL* 4.2 26.0 - - + -
94A LEU* 4.2 25.8 - - + +
105A VAL* 3.9 29.4 - - + -
109A ASP* 4.2 5.8 - - + +
110A ARG* 1.3 78.4 - - - +
112A ALA* 1.3 65.3 + - + +
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Residues in contact with ALA 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ASP* 3.3 9.9 - - - +
29A LEU* 2.9 29.8 + - + +
61A VAL* 3.8 22.9 - - + -
62A HIS 3.3 14.4 - - - +
64A ARG* 3.8 12.3 - - - +
75A ILE* 4.1 7.2 - - + -
92A VAL* 4.3 12.6 - - + -
111A ILE* 1.3 80.7 - - - +
113A GLN* 1.3 63.4 + - - +
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Residues in contact with GLN 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLY* 4.1 18.9 + - - -
27A VAL 3.2 13.0 - - - +
28A ASP* 3.9 10.9 - - - +
29A LEU* 4.5 4.0 - - - +
60A LEU 3.5 0.9 - - - +
61A VAL* 3.3 5.9 - - - +
62A HIS* 2.8 47.5 + - + +
63A PRO 3.2 21.4 + - - -
64A ARG* 4.4 2.9 - - + +
112A ALA* 1.3 77.1 - - - +
114A LEU* 1.3 59.9 + - - +
115A LEU* 3.8 7.4 - - + +
2171A MG 4.1 12.8 - - - -
81B THR* 3.7 31.8 + - - +
83B ASP* 4.9 3.5 - - - +
2170B UMP 4.1 19.4 + - - -
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Residues in contact with LEU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LEU* 4.3 24.5 - - + -
7A ILE* 6.0 1.8 - - + -
19A ARG* 5.0 1.6 + - - -
25A ALA 4.1 0.3 - - - +
26A GLY* 3.2 2.5 - - - -
27A VAL* 2.9 50.0 + - + +
29A LEU* 4.2 16.8 - - + -
51A VAL* 4.4 9.2 - - + -
59A GLY* 4.2 8.1 - - - -
60A LEU 3.4 30.7 - - - +
61A VAL* 4.0 13.5 - - + +
82A ILE* 4.6 3.1 - - + -
90A ILE* 4.2 24.7 - - + -
113A GLN* 1.3 71.6 - - - +
115A LEU* 1.3 64.7 - - - +
116A VAL* 4.4 4.7 + - + +
122B VAL* 6.2 0.2 - - - +
124B LEU* 6.3 0.2 - - + -
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Residues in contact with LEU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ALA* 3.6 37.0 - - + +
26A GLY* 4.2 4.7 - - - +
58A VAL 4.6 0.2 - - - -
59A GLY* 3.3 4.7 - - - -
60A LEU* 2.7 45.8 + - + +
62A HIS* 3.5 43.3 - - + +
113A GLN* 3.8 22.7 - - + -
114A LEU* 1.3 75.6 - - - +
116A VAL* 1.3 66.4 + - - +
117A GLN* 4.2 4.7 - - + -
58B VAL* 4.5 11.9 - - + -
60B LEU* 4.8 1.1 - - + -
81B THR* 4.4 6.1 - - + -
119B VAL* 4.5 9.4 - - + -
3174B TRS 5.2 3.8 - - - -
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Residues in contact with VAL 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 4.4 21.5 - - + -
25A ALA 4.8 1.4 + - - -
53A VAL* 4.8 6.3 - - + -
54A PRO* 4.9 2.7 - - + -
57A MET* 3.8 33.0 - - + -
58A VAL 3.4 12.1 - - - +
59A GLY* 4.6 5.8 - - - -
114A LEU* 4.4 7.8 + - + +
115A LEU* 1.3 79.0 - - - +
117A GLN* 1.3 63.2 + - - +
119B VAL* 3.6 5.4 - - - +
120B GLU* 2.9 36.8 + - + +
122B VAL* 4.0 32.4 - - + +
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Residues in contact with GLN 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A MET* 3.2 8.1 - - - +
58A VAL* 2.8 36.1 + - + +
60A LEU* 3.2 14.3 - - + +
115A LEU* 4.2 4.9 - - + -
116A VAL* 1.3 79.0 - - - +
118A ARG* 1.3 62.2 + - - +
58B VAL* 4.0 12.4 - - - +
60B LEU* 4.2 1.0 - - - +
117B GLN* 3.0 27.3 + - - +
118B ARG 3.1 26.2 + - - +
119B VAL* 4.3 9.0 - - + +
120B GLU* 4.5 4.7 - - - +
3174B TRS 2.8 28.3 + - - -
117C GLN* 3.0 21.4 + - - +
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Residues in contact with ARG 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A THR* 5.0 1.2 + - - -
55A PHE 5.9 0.6 + - - -
56A GLY* 3.6 14.8 + - - +
57A MET* 4.1 25.8 - - + +
117A GLN* 1.3 73.9 - - - +
119A VAL* 1.3 60.8 + - - +
120A GLU* 6.1 0.2 - - - +
118B ARG 5.6 0.6 + - - -
120B GLU* 3.2 29.5 + - - +
117C GLN* 3.1 27.5 + - - +
118C ARG 5.5 0.8 + - - -
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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