Contacts of the strand formed by residues 39 - 48 (chain G) in PDB entry 1SGF
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 GLN 39 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34G TYR* 3.4 4.7 - - - -
35G ARG* 2.8 46.5 + - + +
36G TYR 3.5 0.2 - - - -
38G THR* 1.3 81.4 - - - +
40G TYR* 1.3 66.3 + - - +
39Z GLN* 4.1 18.7 - - + +
40Z TYR* 4.3 24.0 + - + +
151Z PHE* 3.5 38.8 - - - -
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Residues in contact with TYR 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G HIS* 5.4 0.2 + - - -
32G ALA* 4.2 5.6 - - + -
33G VAL 4.6 0.9 - - - -
34G TYR* 3.7 35.0 - + + -
38G THR 4.1 0.2 + - - -
39G GLN* 1.3 77.5 - - - +
41G LEU* 1.3 66.1 + - - +
42G CYS 3.7 31.6 - - - -
43G GLY* 3.7 5.5 + - - -
73G LEU* 4.6 5.8 - - + -
140G GLY* 5.4 0.2 - - - -
141G TRP* 3.7 42.1 + + + +
151G PHE* 4.1 28.9 - + - -
193G GLY* 2.9 29.2 + - - -
38Z THR* 4.4 19.1 + - + +
39Z GLN* 3.5 28.2 + - - +
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Residues in contact with LEU 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B LYS* 5.3 5.6 - - + +
33G VAL* 3.0 26.8 + - + +
34G TYR 4.5 1.1 - - - +
35G ARG* 4.0 25.6 - - + +
40G TYR* 1.3 85.2 - - - +
42G CYS* 1.3 78.6 + - - +
58G CYS* 3.4 27.1 - - + +
60G ASP* 3.5 27.8 - - + +
64G TYR* 4.0 20.9 - - + -
193G GLY* 5.3 4.3 - - - -
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Residues in contact with CYS 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B ARG* 5.1 2.5 - - - -
32G ALA* 3.7 2.6 - - - -
33G VAL* 2.7 34.1 + - + +
40G TYR* 3.7 15.8 + - - -
41G LEU* 1.3 93.3 - - - +
43G GLY* 1.3 62.2 + - - +
54G THR* 4.0 2.5 - - - +
57G HIS* 5.0 2.7 - - - -
58G CYS* 2.0 54.5 - - + -
193G GLY 4.7 3.4 - - - -
195G SER* 3.3 17.5 - - - +
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Residues in contact with GLY 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G HIS* 4.3 9.0 - - - -
31G VAL 3.3 12.3 - - - -
32G ALA* 4.5 0.2 - - - -
33G VAL* 3.7 4.0 - - - +
40G TYR* 3.7 11.6 + - - -
42G CYS* 1.3 75.6 - - - +
44G GLY* 1.3 57.3 + - - -
54G THR* 2.9 22.9 + - - -
193G GLY 4.5 1.4 + - - -
194G ASP 5.1 1.6 - - - -
195G SER 2.7 18.7 + - - +
196G GLY* 3.4 4.6 - - - -
197G GLY* 4.5 3.6 - - - -
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Residues in contact with GLY 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G TRP 3.5 1.7 - - - +
30G HIS* 3.5 9.9 + - - -
31G VAL* 3.0 38.8 + - - -
33G VAL* 4.7 1.1 - - - -
43G GLY* 1.3 74.8 - - - -
45G VAL* 1.3 60.8 + - - +
52G VAL* 4.8 1.1 - - - -
53G LEU 3.4 8.3 - - - -
54G THR* 4.4 2.5 - - - -
196G GLY 3.1 14.4 + - - -
197G GLY* 4.3 1.8 - - - +
198G PRO* 4.3 4.2 - - - +
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Residues in contact with VAL 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G TRP* 3.2 11.9 - - + -
44G GLY* 1.3 74.3 - - - +
46G LEU* 1.3 60.6 + - - +
47G LEU* 3.7 9.1 + - + -
52G VAL* 3.7 4.5 - - - +
53G LEU* 2.8 65.8 + - + +
121G ILE* 3.4 28.9 - - + -
196G GLY 4.8 2.0 - - - +
198G PRO* 3.8 30.7 - - + -
209G LEU* 4.3 9.6 - - + -
212G ILE* 5.0 6.3 - - + -
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Residues in contact with LEU 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28G PRO 4.6 2.5 - - - +
29G TRP* 2.8 22.1 + - - +
31G VAL* 4.4 6.7 - - + +
45G VAL* 1.3 72.3 - - - +
47G LEU* 1.3 59.2 + - - +
48G ASP 3.5 12.6 - - - +
51G TRP 3.4 19.7 - - - +
52G VAL* 3.7 18.6 - - + +
68G LEU* 3.6 24.7 - - + -
108G LEU* 4.6 2.7 - - + -
112G ALA* 4.2 13.7 - - + -
114G ILE* 4.6 1.3 - - + -
118G VAL* 3.8 19.1 - - + -
119G LYS 4.4 6.5 - - - +
120G PRO* 3.3 20.4 - - + +
121G ILE* 2.9 29.5 + - - +
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Residues in contact with LEU 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G VAL* 3.7 20.6 + - + +
46G LEU* 1.3 75.7 - - - +
48G ASP* 1.3 64.9 + - + +
51G TRP* 3.4 9.9 + - + +
52G VAL 5.3 0.4 - - - -
53G LEU* 3.8 35.0 - - + +
105G LEU* 4.0 17.3 - - + -
120G PRO* 3.3 17.1 - - - +
121G ILE* 3.9 20.0 - - + +
123G LEU* 3.8 33.4 - - + -
209G LEU* 4.4 8.1 - - + -
238G ILE* 4.1 10.3 - - + -
242G MET* 5.0 9.0 - - + -
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Residues in contact with ASP 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46G LEU* 3.5 10.2 - - - +
47G LEU* 1.3 80.3 - - + +
49G PRO* 1.3 82.6 - - - +
50G ASN* 2.8 22.1 + - - -
51G TRP* 2.9 45.8 + - + +
120G PRO* 4.7 1.1 - - - -
242G MET* 4.7 15.2 - - + +
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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