Contacts of the strand formed by residues 42 - 53 (chain A) in PDB entry 6QPA
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 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A CSS 4.9 2.7 - - - -
36A THR* 3.4 36.3 - - + +
37A ALA* 3.5 31.9 - - + -
39A HIS 3.0 16.5 + - - +
40A PRO 4.4 3.1 - - - +
41A GLY* 1.3 76.6 - - - +
43A LEU* 1.3 65.0 + - - +
44A GLY* 3.1 41.1 - - - -
45A PHE* 3.7 19.5 - + + -
80A THR* 4.1 11.4 - - + -
81A VAL 3.8 5.6 - - - -
82A TRP* 3.6 22.0 - + + -
305A GLN* 4.6 11.1 + - + -
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Residues in contact with LEU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A GLU* 4.3 7.6 - - - +
6A PRO* 3.7 20.6 - - + -
40A PRO 5.1 0.9 - - - +
41A GLY 3.6 12.8 - - - +
42A PHE* 1.3 79.1 - - - +
44A GLY* 1.3 55.9 + - - +
81A VAL* 2.7 16.5 + - + +
82A TRP 3.7 22.2 - - - +
83A LYS* 3.7 27.1 - - + +
305A GLN* 3.8 12.9 + - - -
307A LEU* 4.1 3.1 - - - +
308A TRP* 3.3 31.6 + - + -
311A HIS* 3.9 28.6 + - + +
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Residues in contact with GLY 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A PHE* 3.1 17.3 - - - -
43A LEU* 1.3 80.8 - - - +
45A PHE* 1.3 60.9 + - - +
81A VAL* 2.8 27.2 + - - +
305A GLN* 3.3 24.2 - - - -
308A TRP* 3.8 9.4 - - - -
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Residues in contact with PHE 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A CSS 3.8 45.8 - - + -
42A PHE* 3.7 22.4 - + + -
44A GLY* 1.3 74.4 - - - +
46A GLU* 1.3 77.0 + - - +
47A GLN* 4.1 9.6 - - + -
78A GLN* 6.4 0.9 - - + -
79A TYR 3.0 18.8 - - - +
80A THR* 4.3 2.0 - - + -
81A VAL* 4.7 2.0 - - - -
303A MET* 3.9 36.3 - - + -
304A GLU* 3.7 3.9 - - - -
305A GLN* 3.1 56.8 + - + +
308A TRP* 4.0 2.3 - - - -
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Residues in contact with GLU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A PHE* 1.3 81.2 - - - +
47A GLN* 1.3 60.3 + - - +
48A LEU* 3.8 13.7 - - + +
77A PHE 3.5 1.9 - - - +
78A GLN* 3.2 4.9 - - - +
79A TYR* 2.7 66.2 + - + +
158A ARG* 4.5 1.1 + - - -
160A VAL* 5.9 0.7 - - - +
256A HIS* 5.6 2.9 - - + -
258A GLU* 5.4 0.4 - - - -
301A PRO* 4.6 4.7 - - - +
303A MET 3.9 2.5 - - - -
304A GLU* 2.6 39.7 - - - +
306A GLY* 4.8 1.7 - - - -
308A TRP* 3.3 33.5 + - + +
309A ARG* 3.6 15.5 + - - -
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Residues in contact with GLN 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A MET* 4.3 26.6 + - - +
29A GLY* 4.6 6.3 - - - -
45A PHE* 4.1 7.5 - - + -
46A GLU* 1.3 69.9 - - - +
48A LEU* 1.3 59.4 + - - +
49A LEU* 6.4 0.2 - - + -
76A MET* 4.2 15.8 - - + +
77A PHE 3.8 2.0 - - - -
78A GLN* 3.4 35.3 - - + +
301A PRO* 3.3 4.7 - - - +
302A MET* 2.7 52.3 + - + +
303A MET* 3.0 48.8 + - + +
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Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A GLU* 4.4 16.4 - - + +
47A GLN* 1.3 75.4 - - - +
49A LEU* 1.3 59.0 + - - +
76A MET* 3.4 8.9 - - - +
77A PHE* 2.8 45.8 + - + +
79A TYR* 3.5 39.9 - - + +
160A VAL* 4.1 27.6 - - + -
162A ILE* 4.0 14.8 - - + -
256A HIS* 5.6 1.1 - - + -
299A PHE* 3.6 16.3 - - + -
300A SER 3.5 1.6 - - - -
301A PRO* 3.8 29.6 - - + -
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ILE* 4.3 7.2 - - + -
22A TYR* 3.6 31.2 - - + +
25A MET* 4.3 11.2 - - + -
47A GLN* 4.1 0.8 + - + -
48A LEU* 1.3 73.1 - - - +
50A GLN* 1.3 71.2 + - - +
51A THR* 3.4 4.8 + - + +
74A MET* 4.0 26.5 - - + -
75A GLY 3.6 15.0 - - - +
76A MET* 3.8 17.5 - - + -
299A PHE* 3.2 2.0 - - - -
300A SER* 2.8 33.7 + - - +
302A MET* 4.0 30.1 - - + -
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Residues in contact with GLN 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LYS* 4.3 4.7 + - - -
49A LEU* 1.3 74.4 - - - +
51A THR* 1.3 63.0 + - - +
52A GLY 3.1 18.6 + - - +
53A ILE* 3.7 17.0 - - - +
68A ARG* 5.0 0.3 - - - +
71A LEU* 3.4 28.4 - - + +
73A PRO 5.0 0.2 - - - +
74A MET* 3.4 26.9 - - - +
75A GLY* 2.8 43.1 + - - +
297A MET* 3.3 28.8 - - + +
298A PHE 3.3 14.8 - - - +
299A PHE* 3.4 11.0 - - + -
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Residues in contact with THR 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU* 3.9 11.4 - - + +
50A GLN* 1.3 76.4 - - - +
52A GLY* 1.3 53.2 + - - +
65A VAL 3.4 5.9 + - - +
66A ASP* 3.6 2.2 - - - -
67A MET* 2.6 31.5 + - - -
68A ARG* 3.4 37.6 + - + +
71A LEU* 4.4 4.0 - - - -
159A THR* 5.7 0.9 - - - +
262A PRO* 5.6 6.1 - - - +
298A PHE* 2.8 26.9 + - - +
299A PHE* 3.8 3.0 + - - -
300A SER* 4.0 20.9 - - - +
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Residues in contact with GLY 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A GLN* 3.1 19.3 + - - +
51A THR* 1.3 81.7 + - - +
53A ILE* 1.3 61.5 + - - +
64A ALA 3.5 6.3 - - - -
65A VAL 3.2 10.5 - - - -
67A MET* 4.0 12.6 - - - -
71A LEU* 4.5 0.9 - - - -
298A PHE* 2.8 27.3 + - - +
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Residues in contact with ILE 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A GLN* 3.7 15.5 - - - +
52A GLY* 1.3 79.3 - - - +
54A HIS* 1.3 66.8 + - - +
55A PRO* 3.5 1.6 - - - +
60A TYR* 3.6 33.2 - - + +
63A GLY* 3.8 17.9 - - - +
64A ALA 2.9 32.6 + - - +
65A VAL* 3.2 16.9 + - - +
67A MET* 4.2 7.2 - - - -
71A LEU* 6.0 0.7 - - + -
295A TYR* 3.3 33.7 - - + +
296A TYR 3.4 12.6 - - - +
297A MET* 4.5 1.1 - - - -
298A PHE* 3.8 8.2 - - - -
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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