Contacts of the strand formed by residues 138 - 141 (chain Q) in PDB entry 6GYK
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 138 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136Q PRO* 3.7 26.4 - - + +
137Q VAL* 1.3 80.6 - - - +
139Q LEU* 1.3 53.8 + - - +
140Q HIS* 4.0 20.0 + - + +
351Q VAL 3.0 2.7 - - - +
352Q MET* 2.7 32.0 - - - -
353Q GLU* 2.9 17.5 + - + +
354Q ASP 4.3 10.6 + - - -
355Q PHE* 6.0 3.2 - - - -
58R ASP* 4.3 23.2 - - - +
59R LEU* 4.0 8.5 - - + +
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Residues in contact with LEU 139 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119Q LEU* 5.6 1.1 - - + -
137Q VAL* 5.0 3.3 - - + +
138Q ARG* 1.3 71.0 - - - +
140Q HIS* 1.3 59.8 + - - +
350Q TRP* 3.7 13.0 - - + -
351Q VAL 2.9 33.4 - - - +
352Q MET* 3.8 9.6 - - + +
395Q PHE* 3.6 30.5 - - + -
59R LEU* 3.8 9.7 - - + +
135R PHE* 3.7 31.2 - - + -
210R LYS 4.4 4.9 + - - +
212R THR* 3.0 50.2 + - + +
214R ILE* 5.2 6.5 - - + -
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Residues in contact with HIS 140 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138Q ARG* 4.2 24.6 - - + +
139Q LEU* 1.3 75.9 - - - +
141Q ARG* 1.3 62.8 + - - +
142Q LYS* 4.4 10.4 + - + +
350Q TRP* 3.2 5.5 - - - -
351Q VAL* 2.9 52.0 + - + +
353Q GLU* 5.4 9.6 - - + -
207R THR* 3.7 20.4 - - + -
209R PRO* 3.8 29.6 - - + -
210R LYS 5.1 1.3 - - - +
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Residues in contact with ARG 141 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140Q HIS* 1.3 72.0 - - - +
142Q LYS* 1.3 57.3 + - - +
346Q GLU* 3.3 48.6 + - - +
348Q TYR* 2.9 36.8 + - + +
349Q PRO* 5.5 0.2 - - - +
350Q TRP* 3.3 55.4 - - + +
393Q TYR* 5.2 4.2 + - - -
137R GLU* 4.3 11.8 + - - +
207R THR* 2.6 24.6 + - - -
208R ILE* 3.1 25.6 + - + +
209R PRO* 4.6 0.2 - - - +
210R LYS* 3.5 30.5 - - + +
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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