Contacts of the strand formed by residues 215 - 224 (chain M) in PDB entry 2GTL
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 PHE 215 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A GLU* 5.8 1.3 - - + -
13A ARG* 3.1 61.0 - - + -
14A GLU* 5.9 0.9 - - - -
10G GLU* 4.9 1.1 - - - -
119M SER* 3.2 19.5 - - - -
120M CYS* 5.2 5.2 - - - -
209M VAL* 3.3 0.6 - - - -
210M VAL* 2.9 35.1 + - + +
213M SER* 2.8 23.4 + - - +
214M LEU* 1.3 77.5 - - - +
216M VAL* 1.3 83.4 + - + +
217M CYS* 3.1 6.2 + - - -
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Residues in contact with VAL 216 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118M THR* 4.3 9.0 - - + +
119M SER* 3.8 13.3 - - - -
207M LYS* 3.8 38.1 - - + -
208M ILE 3.9 3.1 - - - -
209M VAL* 4.4 5.6 - - + +
214M LEU 3.4 4.5 + - - +
215M PHE* 1.3 90.7 - - + +
217M CYS* 1.3 63.9 + - - +
218M ALA 3.3 5.6 - - - +
219M HIS* 5.8 2.0 - - + -
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Residues in contact with CYS 217 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117M TRP* 3.9 10.3 - - + -
118M THR* 3.2 2.4 + - - -
119M SER* 3.0 25.6 + - - -
120M CYS* 2.0 54.5 + - + -
190M TYR* 3.3 28.5 - - + -
208M ILE 2.7 16.5 + - - +
210M VAL* 4.2 18.2 - - - -
215M PHE* 3.1 6.2 + - - -
216M VAL* 1.3 73.7 - - - +
218M ALA* 1.3 60.3 + - - +
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Residues in contact with ALA 218 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115M ALA* 5.0 0.7 - - + -
116M THR 3.8 7.2 - - - +
117M TRP* 3.3 46.0 - - + +
118M THR* 4.0 7.4 - - - -
207M LYS* 3.4 5.7 - - - +
208M ILE* 2.8 39.7 + - + +
216M VAL* 3.3 4.5 - - - +
217M CYS* 1.3 79.4 + - - +
219M HIS* 1.3 61.3 + - - +
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Residues in contact with HIS 219 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115M ALA* 4.4 0.2 - - - -
116M THR* 3.1 39.2 + - + +
118M THR* 4.7 5.5 - - + +
205M ASP* 3.3 31.7 + - - -
206M CYS 3.9 13.0 + - - -
207M LYS* 4.2 12.6 - - + +
216M VAL* 5.8 2.7 - - + -
218M ALA* 1.3 77.0 - - - +
220M PHE* 1.3 67.8 + - - +
221M ASN* 3.6 17.9 - - + -
61N HIS* 5.7 4.9 + + - -
74N GLN* 3.9 23.1 + - - -
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Residues in contact with PHE 220 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111M TYR 4.7 1.8 - - - -
112M THR* 4.4 2.2 - - - -
113M GLY* 3.8 19.7 - - - -
114M LEU 3.3 12.1 - - - +
115M ALA* 3.3 22.9 - - + -
116M THR* 5.2 0.2 - - - -
128M ALA* 3.6 31.4 - - + -
130M VAL* 4.5 14.1 - - + -
151M LEU* 5.2 2.7 - - + -
192M VAL* 4.6 6.7 - - + -
206M CYS* 2.8 67.6 + - + +
207M LYS 4.5 0.9 - - - -
208M ILE* 3.8 26.9 - - + -
219M HIS* 1.3 80.8 + - - +
221M ASN* 1.3 58.8 + - - +
222M ALA* 3.5 18.8 - - + -
74N GLN* 6.2 0.2 - - - -
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Residues in contact with ASN 221 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113M GLY* 3.4 5.2 - - - -
114M LEU 4.7 1.8 + - - -
198M LEU* 5.5 11.1 - - - +
203M HIS* 5.6 4.7 - - - +
204M ALA 3.7 11.5 + - - +
205M ASP* 3.9 17.3 + - - +
206M CYS 4.7 0.9 - - - +
219M HIS* 3.6 9.5 - - + -
220M PHE* 1.3 70.6 - - - +
222M ALA* 1.3 68.2 + - - +
71N GLY 3.2 23.3 + - - +
72N ASN* 3.0 23.2 + - - +
74N GLN* 3.8 30.1 + - + +
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Residues in contact with ALA 222 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111M TYR* 4.2 7.0 - - + -
112M THR 3.1 26.5 - - - +
203M HIS* 3.5 5.9 - - - +
204M ALA* 2.8 39.4 + - + +
206M CYS* 4.0 13.7 - - - -
220M PHE* 3.4 20.7 + - + -
221M ASN* 1.3 81.2 - - - +
223M GLN* 1.3 60.8 + - - +
72N ASN* 4.7 0.7 - - - -
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Residues in contact with GLN 223 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111M TYR* 3.2 4.7 - - - -
112M THR* 2.8 36.8 + - - +
202M ASP* 3.4 11.9 - - + +
203M HIS* 3.9 29.3 + - + +
222M ALA* 1.3 74.5 - - - +
224M ARG* 1.3 75.6 + - - +
225M TYR* 3.9 32.7 + - + -
72N ASN* 4.3 23.0 - - + +
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Residues in contact with ARG 224 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103M ASN* 2.7 30.4 + - - +
104M ILE* 4.3 0.6 - - - +
106M HIS* 4.8 4.2 - - - +
109M SER* 3.0 24.5 + - - +
110M SER 3.4 13.2 - - - +
111M TYR* 3.3 30.1 + - + -
201M ASP* 2.7 30.3 + - - +
202M ASP* 2.9 43.2 + - + +
223M GLN* 1.3 80.9 + - - +
225M TYR* 1.3 84.5 + - - +
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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