Contacts of the strand formed by residues 113 - 124 (chain A) in PDB entry 2YD4
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 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A PRO* 4.8 1.1 - - - -
32A PRO* 3.6 12.4 - - - +
109A GLN* 3.4 5.4 - - - +
110A ASN* 3.1 31.6 + - - +
111A PRO 3.5 1.6 + - - -
112A HIS* 1.3 82.1 - - - +
114A GLU* 1.3 60.6 + - - -
115A VAL* 5.7 1.1 - - - -
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Residues in contact with GLU 114 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A VAL* 3.4 31.3 - - + +
108A ALA 3.3 5.8 - - - +
109A GLN* 3.7 27.7 + - + +
113A GLY* 1.3 75.3 - - - +
115A VAL* 1.3 67.0 + - - +
116A THR* 5.4 1.4 + - - +
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Residues in contact with VAL 115 (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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31A PRO* 6.1 1.8 - - + -
32A PRO* 3.8 36.6 - - + +
34A PHE* 3.6 22.4 - - + -
107A VAL* 3.3 4.2 - - - +
108A ALA* 2.8 40.7 + - + +
113A GLY* 5.7 0.9 - - - -
114A GLU* 1.3 83.6 - - - +
116A THR* 1.3 63.0 + - - +
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Residues in contact with THR 116 (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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34A PHE* 4.0 1.3 - - - -
105A GLU* 3.8 21.1 - - + -
106A CYS 3.3 8.5 - - - -
107A VAL* 3.6 16.2 - - + +
114A GLU* 5.4 1.0 + - - +
115A VAL* 1.3 79.4 + - - +
117A VAL* 1.3 80.6 + - - +
118A HIS* 3.8 30.1 - - - +
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Residues in contact with VAL 117 (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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34A PHE* 3.5 46.7 - - + -
37A LYS* 3.5 33.2 - - + +
38A PRO* 3.5 28.4 - - + +
105A GLU* 3.5 3.8 - - - -
106A CYS* 2.8 34.0 + - + +
116A THR* 1.3 76.1 - - - +
118A HIS* 1.3 66.7 + - - +
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Residues in contact with HIS 118 (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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37A LYS* 5.1 5.3 + - - +
38A PRO* 4.1 13.9 - - - +
40A ASP* 4.6 2.3 - - - +
103A ILE* 3.7 22.9 - - + -
104A TYR 3.3 4.0 - - - -
105A GLU* 3.9 26.3 + - + +
116A THR* 3.8 29.9 + - + +
117A VAL* 1.3 79.5 - - - +
119A ALA* 1.3 62.8 + - - +
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Residues in contact with ALA 119 (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 PRO* 3.8 20.4 - - + +
39A VAL 4.0 5.2 - - - +
40A ASP* 3.6 6.1 - - - +
51A PHE* 3.5 31.9 - - + -
65A TRP* 4.6 4.5 - - + -
102A ASN 4.0 0.5 - - - +
103A ILE* 3.5 3.5 - - - -
104A TYR* 2.8 36.9 + - + +
118A HIS* 1.3 76.9 - - - +
120A LYS* 1.3 62.3 + - - +
121A LEU 4.0 0.2 + - - -
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Residues in contact with LYS 120 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A ASP* 2.9 30.2 + - - +
41A GLN 3.0 27.4 + - - +
51A PHE* 3.7 3.9 - - - -
102A ASN 3.6 9.9 - - - +
103A ILE* 4.4 18.4 - - + +
119A ALA* 1.3 73.0 - - - +
121A LEU* 1.3 71.2 + - - +
122A THR* 4.4 12.6 + - - +
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Residues in contact with LEU 121 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A GLN* 3.5 12.1 - - + +
43A GLY 4.7 1.8 - - - +
49A ALA* 3.8 26.5 - - + -
51A PHE* 3.9 8.1 - - + -
92A ILE* 4.4 15.3 - - + -
95A LEU* 4.0 14.6 - - + -
100A ASP* 3.5 31.9 - - + +
101A GLU* 3.2 22.0 - - - +
102A ASN 2.9 12.7 + - - +
104A TYR* 3.8 23.3 - - + +
119A ALA 4.0 0.4 + - - -
120A LYS* 1.3 77.4 - - - +
122A THR* 1.3 77.2 + - - +
123A VAL* 3.9 10.8 - - + -
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Residues in contact with THR 122 (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 GLN 2.9 12.6 + - - +
42A ILE* 4.1 19.3 - - + +
43A GLY 2.9 25.1 + - - -
101A GLU* 3.4 15.0 - - - +
120A LYS* 4.4 18.2 + - - +
121A LEU* 1.3 75.4 + - - +
123A VAL* 1.3 69.0 + - - +
124A LEU* 3.9 22.7 - - + -
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Residues in contact with VAL 123 (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 GLY 3.5 3.1 - - - +
44A VAL 4.1 1.1 - - - -
45A SER* 3.6 28.9 - - - +
95A LEU* 4.0 22.9 - - + -
96A ARG 4.0 10.5 - - - +
97A THR* 2.6 51.5 + - - +
100A ASP* 4.3 3.4 - - + -
101A GLU* 2.9 19.9 + - + +
121A LEU* 3.9 24.2 - - + -
122A THR* 1.3 79.2 - - - +
124A LEU* 1.3 62.8 + - - +
125A ARG 4.1 0.2 + - - -
128A GLN* 4.7 1.6 - - - +
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Residues in contact with LEU 124 (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 ILE* 3.8 25.1 - - + -
43A GLY 2.9 11.6 + - - +
44A VAL* 3.4 4.3 - - - +
45A SER* 2.9 26.0 + - - -
97A THR* 4.6 0.4 - - - -
101A GLU* 5.3 0.4 - - - +
122A THR* 3.9 21.5 - - + -
123A VAL* 1.3 75.9 - - - +
125A ARG* 1.3 64.5 + - - +
128A GLN* 3.8 18.4 - - + +
129A LEU* 3.8 17.9 - - + -
130A PRO* 3.8 29.6 - - + -
133A PHE* 4.2 5.6 - - + -
212A ALA 4.9 0.7 - - - +
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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