Contacts of the strand formed by residues 131 - 140 (chain D) in PDB entry 1GGE
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 GLY 131 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D ALA 3.7 0.4 + - - -
130D ARG* 1.3 76.5 - - - +
132D SER* 1.3 62.0 + - - -
165D ARG* 3.2 22.6 + - - +
166D PHE 3.0 13.5 - - - -
167D SER* 3.8 1.1 - - - -
266D TYR* 5.0 2.0 - - - -
319D ARG* 2.8 24.7 + - - +
382D PHE* 3.4 2.8 - - - -
386D ASN* 3.1 15.9 + - - +
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Residues in contact with SER 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D GLY* 1.3 72.8 - - - -
133D ALA* 1.3 61.9 + - - +
165D ARG* 4.2 0.6 - - - +
166D PHE* 2.8 36.2 + - - +
177D ASP* 4.8 2.4 + - - -
266D TYR* 4.0 13.6 + - - -
319D ARG* 3.1 48.7 + - - +
322D LEU* 3.8 18.6 - - - -
382D PHE* 4.7 1.1 - - - -
386D ASN* 3.5 3.1 - - - +
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Residues in contact with ALA 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D SER* 1.3 76.4 - - - +
134D ALA* 1.3 66.5 + - - +
163D PHE* 3.4 29.8 - - + -
164D VAL 3.0 14.1 - - - +
165D ARG* 3.9 7.4 - - + -
322D LEU* 4.4 7.4 - - - +
323D TRP* 5.0 4.0 - - - -
378D ASN* 4.6 2.3 - - - +
379D PRO* 3.4 21.1 - - + +
382D PHE* 5.2 0.8 - - - -
386D ASN* 3.2 20.5 - - + +
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Residues in contact with ALA 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D ALA* 1.3 79.1 - - - +
135D HIS* 1.3 65.2 + - - +
136D GLY 4.2 0.2 + - - -
163D PHE* 3.5 9.8 - - - -
164D VAL* 2.9 34.7 + - - +
322D LEU* 4.8 6.7 - - + +
326D ILE* 3.4 32.5 - - + -
375D LEU* 4.3 12.6 - - + +
377D ARG 3.7 6.7 - - - +
378D ASN* 4.4 2.5 - - - +
379D PRO* 4.3 2.5 - - - -
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Residues in contact with HIS 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D ASN* 4.7 2.6 + - - +
64D LYS* 4.8 9.5 - - + +
65D LEU* 3.4 45.2 - - + +
68D LEU* 3.9 9.6 - - + -
134D ALA* 1.3 75.8 - - - +
136D GLY* 1.3 59.5 + - - +
162D VAL 3.5 9.2 + - - +
163D PHE* 3.6 29.0 - + + +
375D LEU* 3.5 5.4 - - - -
376D ASN* 3.0 21.2 + - - -
377D ARG* 2.8 24.0 + - + +
378D ASN 4.2 2.0 - - - -
379D PRO* 4.1 12.3 - - + -
385D GLU* 2.7 27.7 + - - -
433D ILE* 3.6 14.8 - - + -
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Residues in contact with GLY 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D ASN* 3.2 16.4 + - - +
135D HIS* 1.3 77.7 - - - +
137D TYR* 1.3 62.9 + - - -
161D PRO* 3.5 0.3 - - - +
162D VAL* 2.8 35.2 + - - +
374D VAL 3.0 14.8 - - - -
375D LEU* 3.9 1.8 - - - -
376D ASN* 3.7 10.1 - - - -
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Residues in contact with TYR 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D ASN* 5.0 8.3 - - + +
136D GLY* 1.3 76.5 - - - +
138D PHE* 1.3 65.7 + - - +
139D GLN* 4.3 10.5 - - + -
159D ILE* 3.8 41.5 - - + -
160D THR 3.4 7.6 - - - +
161D PRO* 4.6 1.8 - - + -
162D VAL* 3.8 5.9 - - - +
372D LYS* 3.9 2.4 - - - +
373D MET* 3.3 2.1 - - - +
374D VAL* 2.9 67.0 + - + +
376D ASN* 3.8 26.9 - - - -
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Residues in contact with PHE 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D TYR* 1.3 78.2 - - - +
139D GLN* 1.3 65.8 + - - +
140D PRO* 3.7 28.3 - - + -
152D PHE* 3.8 25.1 - + - -
153D LEU* 3.8 20.4 - - + -
158D LYS 3.9 0.3 - - - +
159D ILE* 3.5 2.9 - - - +
160D THR* 2.7 42.0 + - - +
162D VAL* 4.0 5.8 - - + -
189D PHE* 3.7 29.2 - + + -
293D TRP* 4.5 1.8 - + - -
336D LEU* 3.9 26.2 - - + -
370D VAL* 4.6 0.7 - - + -
371D GLY* 3.9 21.5 - - - -
372D LYS 3.3 19.5 - - - -
373D MET* 4.3 9.2 - - + -
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Residues in contact with GLN 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D TYR* 4.3 10.8 - - + -
138D PHE* 1.3 84.9 - - - +
140D PRO* 1.3 72.4 - - + +
141D TYR* 4.7 2.3 - - + -
156D PRO 2.7 30.5 + - - +
157D ASN* 4.0 12.7 + - - +
158D LYS 3.9 2.7 - - - +
159D ILE* 3.3 30.9 - - + +
371D GLY* 3.3 0.2 - - - -
372D LYS* 3.0 30.5 + - + +
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Residues in contact with PRO 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D PHE* 3.7 5.1 - - + -
139D GLN* 1.3 93.0 - - + +
141D TYR* 1.3 64.5 + - - +
142D LYS 3.7 15.0 - - - +
144D LEU* 5.5 0.2 - - + -
152D PHE 3.6 20.4 - - - +
153D LEU* 4.1 23.8 - - + -
155D ASP 3.3 24.9 - - - +
156D PRO* 3.3 19.4 - - - +
158D LYS 3.5 16.6 - - - +
370D VAL* 3.3 11.7 - - + +
371D GLY* 3.9 2.0 - - - -
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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