Contacts of the strand formed by residues 61 - 71 (chain D) in PDB entry 3STJ
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 61 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31D VAL* 3.7 25.4 - - + -
32D GLU* 3.4 6.2 - - - +
33D GLY* 3.2 32.9 + - - -
34D THR 3.3 42.4 - - - -
59D GLN 4.6 1.1 - - - +
60D PRO* 1.3 76.1 - - - +
62D GLU* 1.3 67.8 + - - +
63D GLY* 3.9 11.9 - - - -
86D GLN* 3.7 47.3 - - + -
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Residues in contact with GLU 62 (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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30D ARG* 3.1 32.3 + - + +
31D VAL 3.3 3.8 - - - +
32D GLU* 3.2 36.7 - - + +
61D PHE* 1.3 78.1 - - - +
63D GLY* 1.3 59.4 + - - +
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Residues in contact with GLY 63 (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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29D VAL 4.6 0.2 - - - -
30D ARG* 3.6 6.4 - - - +
31D VAL* 2.8 41.5 + - - +
61D PHE* 3.9 13.8 - - - -
62D GLU* 1.3 73.0 - - - +
64D LEU* 1.3 61.6 + - - +
83D VAL* 5.9 1.8 - - - -
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Residues in contact with LEU 64 (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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28D SER* 3.8 11.7 - - - +
29D VAL 3.5 7.2 - - - +
30D ARG* 4.4 20.4 - - + +
63D GLY* 1.3 73.7 - - - +
65D GLY* 1.3 76.6 + - - +
83D VAL* 5.0 2.9 - - - -
146D ASN* 3.5 34.3 - - + +
149D GLY* 4.2 18.8 - - - +
185D GLY* 4.0 13.3 - - - -
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Residues in contact with GLY 65 (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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28D SER* 3.7 3.3 - - - -
29D VAL* 2.9 29.9 + - - +
64D LEU* 1.3 84.2 - - - +
66D SER* 1.3 62.0 + - - -
83D VAL* 4.1 14.6 - - - +
146D ASN* 3.7 1.7 - - - +
185D GLY* 3.5 16.4 - - - -
187D SER* 3.9 7.0 - - - -
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Residues in contact with SER 66 (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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26D VAL* 5.1 0.7 - - - -
27D VAL 3.3 11.5 + - - -
29D VAL* 3.4 9.2 - - - +
65D GLY* 1.3 70.6 - - - -
67D GLY* 1.3 55.2 + - - +
79D THR* 2.8 27.5 + - - -
145D GLY* 3.1 6.5 - - - -
146D ASN* 2.7 34.7 + - - +
185D GLY 3.3 4.7 + - - -
186D ASN 3.9 1.8 - - - -
187D SER 2.8 12.3 + - - +
188D GLY* 3.4 3.5 - - - -
189D GLY* 3.4 25.8 - - - -
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Residues in contact with GLY 67 (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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26D VAL* 3.4 10.7 - - - +
27D VAL* 2.8 44.8 + - - +
29D VAL* 3.7 2.8 - - - +
66D SER* 1.3 75.0 - - - +
68D VAL* 1.3 64.1 + - - -
77D VAL* 3.9 6.3 - - - -
78D LEU 3.3 11.9 - - - -
79D THR* 4.4 0.4 - - - -
188D GLY 3.3 3.1 + - - -
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Residues in contact with VAL 68 (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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25D ALA 3.7 6.1 - - - +
26D VAL* 4.7 1.3 - - + -
67D GLY* 1.3 78.9 - - - +
69D ILE* 1.4 64.9 + - - +
70D ILE* 3.3 3.3 + - + +
77D VAL* 3.4 5.9 - - - +
78D LEU* 2.8 39.3 + - + +
127D ILE* 3.7 42.0 - - + -
188D GLY 3.7 1.6 - - - +
190D ALA* 3.6 31.2 - - + +
198D LEU* 4.1 9.4 - - + -
201D ILE* 3.6 29.4 - - + -
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Residues in contact with ILE 69 (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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24D PRO 4.0 8.5 - - - +
25D ALA* 2.9 16.6 + - - +
27D VAL* 3.6 26.9 - - + -
68D VAL* 1.4 68.1 - - - +
70D ILE* 1.3 60.3 + - - +
71D ASN 3.8 6.3 - - - +
72D ALA* 3.8 28.3 - - - +
75D GLY* 5.2 0.2 - - - -
76D TYR 3.5 7.6 - - - +
77D VAL* 4.2 14.4 - - + +
94D LEU* 4.2 7.4 - - + -
118D ILE* 4.5 3.8 - - + -
124D LEU* 3.9 25.1 - - + -
125D THR 3.3 27.6 - - - +
126D GLN* 3.4 0.6 - - - -
127D ILE* 2.9 32.6 + - - +
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Residues in contact with ILE 70 (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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68D VAL* 3.3 6.6 + - + +
69D ILE* 1.3 74.1 - - - +
71D ASN* 1.4 62.9 + - + +
76D TYR* 2.8 31.6 + - + +
78D LEU* 3.6 33.9 - - + +
115D LEU* 4.3 10.8 - - + -
126D GLN* 3.9 16.5 + - - +
127D ILE* 4.4 12.5 - - + +
129D ILE* 3.7 34.3 - - + +
198D LEU* 5.3 2.2 - - + -
225D ARG* 4.9 6.7 - - + -
228D ALA* 4.1 14.8 - - + -
232D ILE* 6.2 1.3 - - + -
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Residues in contact with ASN 71 (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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69D ILE* 3.8 4.0 - - - +
70D ILE* 1.4 81.1 - - + +
72D ALA* 1.3 52.8 + - - +
73D SER* 3.1 15.1 + - - -
74D LYS* 3.0 43.7 + - - +
75D GLY* 2.8 30.8 + - - -
76D TYR* 2.9 34.0 + - + -
126D GLN* 3.4 8.5 + - - +
232D ILE* 6.1 1.0 - - - +
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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