Contacts of the strand formed by residues 44 - 52 (chain n) in PDB entry 5GJQ
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 44 (chain n).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41n CYS* 3.0 24.4 + - - -
43n ASP* 1.3 80.2 - - - +
45n VAL* 1.3 68.8 + - - +
140n TYR* 4.0 3.1 - - - -
146n ALA* 3.6 20.3 - - - +
186n CYS* 3.6 8.5 - - - -
216n VAL 3.2 14.1 - - - -
217n GLY* 3.7 4.0 - - - -
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Residues in contact with VAL 45 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39n ILE 3.6 17.3 - - - +
40n ARG* 4.1 8.5 - - + -
44n GLY* 1.3 82.1 - - - +
46n VAL* 1.3 72.6 + - - +
47n PHE* 4.1 26.5 - - + -
138n GLY* 4.7 0.4 - - - -
139n SER 3.9 13.7 - - - +
146n ALA* 4.2 0.2 - - + -
147n GLN 3.6 32.1 - - - +
148n LEU* 4.2 13.5 - - + -
186n CYS* 3.8 1.9 - - - -
214n SER 3.9 0.3 - - - +
215n TRP 3.7 0.3 - - - -
216n VAL* 2.9 41.4 + - + +
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Residues in contact with VAL 46 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38n GLY* 3.3 3.5 - - - -
39n ILE* 3.0 34.0 + - - +
41n CYS* 5.1 0.2 - - - -
45n VAL* 1.3 79.9 - - - +
47n PHE* 1.3 73.0 + - - +
48n GLY 4.3 0.2 + - - -
186n CYS* 3.9 34.1 - - - +
189n ILE* 4.1 18.6 - - + -
190n VAL* 4.1 24.0 - - + -
193n VAL* 4.0 20.3 - - + +
213n LEU* 5.0 2.7 - - + -
214n SER 3.3 10.3 - - - +
215n TRP* 4.4 8.1 - - + -
227n VAL* 5.3 1.3 - - + -
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Residues in contact with PHE 47 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37n ILE 3.8 2.2 - - - -
38n GLY* 3.7 14.6 - - - -
45n VAL* 4.1 9.6 - - + -
46n VAL* 1.3 78.3 - - - +
48n GLY* 1.3 58.1 + - - +
66n LEU* 4.0 13.0 - - + -
74n GLY* 4.0 12.6 - - - -
75n MET 4.7 0.4 - - - -
76n ALA* 3.9 16.6 - - + -
136n MET* 3.7 23.3 - - + -
137n LEU 4.0 1.6 - - - -
138n GLY* 3.5 29.4 - - - -
148n LEU* 3.5 33.9 - - + -
193n VAL* 4.5 0.9 - - - -
212n GLU 4.3 0.2 - - - -
213n LEU* 3.2 10.2 - - - +
214n SER* 2.8 43.9 + - - -
216n VAL* 4.7 3.1 - - + -
224n HIS* 4.0 22.4 - + - -
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Residues in contact with GLY 48 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36n ALA* 3.4 0.7 - - - +
37n ILE* 2.8 40.8 + - - +
47n PHE* 1.3 75.2 - - - +
49n VAL* 1.3 69.2 + - - +
76n ALA* 5.4 0.9 - - - +
193n VAL* 3.8 19.8 - - - +
197n ILE* 4.7 2.9 - - - -
211n LEU* 4.9 2.2 - - - -
212n GLU 3.2 8.1 - - - -
213n LEU* 4.0 1.6 - - - -
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Residues in contact with VAL 49 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35n THR 4.1 3.8 - - - +
36n ALA* 3.8 15.3 - - + -
48n GLY* 1.3 80.9 - - - +
50n GLU* 1.3 68.5 + - - +
51n LYS* 3.3 7.0 + - + +
65n ARG* 3.6 46.0 - - + +
66n LEU* 3.7 31.0 - - + -
76n ALA* 4.8 1.6 - - + -
77n VAL 5.2 0.2 - - - +
197n ILE* 4.7 1.1 - - - -
210n GLU 3.5 1.9 - - - +
211n LEU* 3.5 9.5 - - - +
212n GLU* 2.9 45.9 + - + +
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Residues in contact with GLU 50 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34n SER* 3.2 28.8 + - - -
35n THR* 3.0 45.4 + - - +
49n VAL* 1.3 71.1 - - - +
51n LYS* 1.3 57.3 + - - +
52n LEU* 3.4 18.3 + - + +
167n LYS* 5.6 1.9 - - - +
197n ILE* 4.1 19.1 - - + +
200n VAL* 4.6 4.8 - - + +
201n HIS* 2.4 45.3 + - + +
202n ASP 4.4 0.3 + - - -
206n ASP* 4.2 6.4 - - - +
209n PHE* 3.7 23.6 - - + -
210n GLU 4.1 2.2 - - - -
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Residues in contact with LYS 51 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34n SER* 5.0 1.1 - - - -
49n VAL* 3.3 10.7 + - + +
50n GLU* 1.3 70.1 - - - +
52n LEU* 1.3 72.6 + - - +
53n VAL* 3.4 0.9 + - - +
61n GLY* 3.5 25.3 + - - +
62n SER 3.1 21.9 + - - +
63n ASN* 3.1 28.6 + - + +
64n LYS* 4.5 0.4 - - - +
65n ARG* 4.3 10.5 - - - +
209n PHE* 4.3 1.1 - - - -
210n GLU* 2.9 69.6 + - - +
212n GLU* 3.6 31.1 + - + +
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Residues in contact with LEU 52 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34n SER* 3.8 24.7 + - - -
50n GLU* 3.4 33.5 + - + +
51n LYS* 1.3 80.2 - - - +
53n VAL* 1.3 62.1 + - - +
54n LEU* 3.6 29.7 + - + +
58n TYR* 6.1 0.2 - - - -
167n LYS* 4.4 7.9 - - - +
201n HIS* 4.1 0.4 - - + -
206n ASP* 3.6 39.7 - - + +
208n ALA 4.9 2.7 - - - +
209n PHE* 4.0 13.0 - - + -
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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