Contacts of the strand formed by residues 57 - 69 (chain A) in PDB entry 5TIN
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 ASP 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A SER 4.3 2.4 - - - +
51A ILE* 3.6 2.6 - - - +
52A ALA* 2.9 34.2 + - - +
55A THR* 2.7 27.5 + - - -
56A MET* 1.3 79.0 - - - +
58A TYR* 1.3 65.3 + - - +
104A LYS* 2.9 36.4 + - + +
135A THR* 3.9 16.0 - - + +
136A LEU 3.1 16.6 - - - +
138A CYS* 3.9 6.5 + - - +
140A MET* 4.5 1.9 - - - +
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Residues in contact with TYR 58 (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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48A PHE* 3.7 33.9 - + - -
50A SER 3.6 8.3 - - - -
51A ILE* 3.9 23.6 - - + -
57A ASP* 1.3 74.9 - - - +
59A ARG* 1.3 62.5 + - - +
60A VAL* 3.8 20.0 - - + -
134A LEU 3.7 0.2 - - - +
135A THR* 3.3 7.2 - - - +
136A LEU* 2.9 69.5 + - + +
137A SER 4.3 0.9 - - - -
138A CYS* 3.7 17.7 - - + -
152A CYS* 3.6 23.1 - - + -
153A ILE 2.7 30.8 + - - -
154A MET* 4.0 0.3 + - - +
214A PHE* 4.0 11.4 - + - -
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Residues in contact with ARG 59 (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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47A SER* 5.2 1.7 + - - +
48A PHE* 3.5 0.5 - - - -
49A GLY 2.9 39.8 + - - +
50A SER* 3.3 36.4 + - - +
58A TYR* 1.3 76.9 - - - +
60A VAL* 1.3 73.5 + - - +
133A THR* 3.8 24.2 - - + -
134A LEU 3.2 10.3 - - - +
135A THR* 4.2 15.5 + - + +
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Residues in contact with VAL 60 (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 ILE* 4.9 2.9 - - + -
47A SER* 3.3 8.3 - - - +
48A PHE* 3.7 28.5 - - + -
58A TYR* 3.8 17.5 - - + -
59A ARG* 1.3 83.3 - - - +
61A ASN* 1.3 59.3 + - - +
62A ILE* 3.8 22.7 - - + -
132A LEU 3.8 0.2 - - - +
133A THR* 3.3 6.2 - - - +
134A LEU* 2.9 55.2 + - + +
136A LEU* 4.0 14.1 - - + -
154A MET* 4.0 11.9 - - + -
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Residues in contact with ASN 61 (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 ASN* 2.8 49.9 + - - +
47A SER* 3.0 31.7 + - - +
60A VAL* 1.3 72.1 - - - +
62A ILE* 1.3 66.4 + - - +
109A HIS* 3.3 20.2 + - - -
131A ARG* 3.1 24.6 + - - +
132A LEU 3.3 6.5 + - - -
133A THR* 2.9 26.5 + - + +
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Residues in contact with ILE 62 (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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43A ILE* 4.3 17.0 - - + -
44A PHE 3.2 13.0 - - - +
45A ILE* 4.3 15.5 - - + -
46A ASN 4.4 0.4 - - - +
60A VAL* 3.8 24.0 - - + -
61A ASN* 1.3 79.2 - - - +
63A PHE* 1.3 70.8 + - - +
64A LEU* 4.2 13.5 - - + +
100A PHE* 4.1 17.3 - - + -
131A ARG* 3.3 5.8 - - - +
132A LEU* 2.9 45.9 + - + +
134A LEU* 4.0 22.4 - - + -
154A MET* 4.5 9.2 - - + -
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Residues in contact with PHE 63 (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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43A ILE* 3.3 6.6 - - - +
44A PHE* 2.9 52.6 + + + -
46A ASN* 4.7 16.4 - - - -
61A ASN* 4.7 4.5 - - - -
62A ILE* 1.3 80.6 - - - +
64A LEU* 1.3 60.6 + - - +
65A ARG* 3.7 32.0 - - - +
129A SER* 4.0 8.5 - - - +
130A ILE 3.5 4.5 - - - +
131A ARG* 3.8 36.6 - - + -
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Residues in contact with LEU 64 (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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41A CYS* 5.0 1.8 - - + -
42A ASN 4.0 2.2 - - - +
43A ILE* 4.0 20.4 - - + -
62A ILE* 3.9 12.0 - - + -
63A PHE* 1.3 70.8 - - - +
65A ARG* 1.3 69.0 + - - +
66A GLN* 3.8 23.0 + - + +
98A LEU* 3.9 16.8 - - + -
100A PHE* 4.2 9.6 - - + -
128A TYR 3.5 1.9 - - - +
129A SER* 3.2 3.3 - - - -
130A ILE* 2.8 45.9 + - + +
132A LEU* 4.2 5.2 - - + -
156A LEU* 4.0 21.1 - - + -
112B THR* 3.8 28.9 - - + -
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Residues in contact with ARG 65 (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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40A THR 3.7 0.4 - - - +
41A CYS* 3.3 8.0 - - - +
42A ASN* 2.7 81.7 + - - +
44A PHE* 3.7 26.6 - - - +
63A PHE* 3.7 22.0 - - - +
64A LEU* 1.3 75.7 - - - +
66A GLN* 1.3 65.1 + - - +
67A LYS* 5.4 0.7 - - - -
127A LEU* 4.1 17.0 - - + -
128A TYR 3.4 3.4 - - - +
129A SER* 3.2 29.3 + - - +
177A GLN* 2.9 20.2 + - - -
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Residues in contact with GLN 66 (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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39A VAL* 4.1 11.1 - - + +
40A THR 3.4 2.7 - - - -
41A CYS* 4.3 9.4 - - - -
64A LEU* 3.8 21.2 - - + +
65A ARG* 1.3 78.8 - - - +
67A LYS* 1.3 62.6 + - - +
68A TRP* 3.8 17.9 - - + -
96A PRO* 3.4 33.1 + - - +
98A LEU* 3.8 25.6 - - + +
126A VAL 3.8 0.5 - - - +
127A LEU* 3.6 3.3 - - - +
128A TYR* 2.9 58.9 + - + +
130A ILE* 5.2 1.2 - - - +
168A PHE* 4.8 0.2 - - - -
112B THR* 4.7 6.1 + - - +
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Residues in contact with LYS 67 (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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38A GLN 3.7 0.7 - - - +
39A VAL* 3.3 2.8 - - - -
40A THR* 2.8 49.4 + - + +
42A ASN* 4.1 9.1 - - - +
65A ARG 5.4 0.7 - - - -
66A GLN* 1.3 80.5 - - - +
68A TRP* 1.3 66.8 + - - +
126A VAL 3.2 10.8 - - - +
127A LEU* 4.0 26.2 - - + -
171A GLN* 2.8 32.4 + - + +
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Residues in contact with TRP 68 (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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30A PRO* 4.3 3.1 - - + -
37A VAL* 4.0 10.5 - - + -
38A GLN 3.6 16.2 - - - +
39A VAL* 4.2 4.7 - - + -
66A GLN* 3.8 24.5 - - + -
67A LYS* 1.3 85.7 - - - +
69A ASN* 1.3 75.4 + - - +
70A ASP* 4.3 6.7 + - - +
93A ILE* 4.6 4.3 - - + -
94A TRP* 3.5 48.9 + + - -
95A LYS* 3.8 8.3 - - + -
96A PRO* 3.6 32.8 - - + -
125A ASN* 3.4 5.8 - - - +
126A VAL* 2.8 64.3 + - + +
128A TYR* 3.8 15.5 - + + -
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Residues in contact with ASN 69 (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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30A PRO* 3.4 19.6 - - - +
31A ASN* 4.9 4.8 + - - +
37A VAL* 5.0 3.7 - - - +
38A GLN 4.7 2.4 + - - -
68A TRP* 1.3 77.3 - - - +
70A ASP* 1.3 59.5 + - - +
71A PRO* 3.3 24.8 - - - +
123A ASN* 3.0 29.2 + - - +
124A GLY 3.3 1.6 - - - -
125A ASN* 2.9 31.4 + - - +
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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