Contacts of the strand formed by residues 112 - 128 (chain A) in PDB entry 2EIE
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 LYS 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A SER* 3.3 5.9 - - - -
70A MET* 2.8 52.6 + - + +
72A PRO* 4.6 2.0 - - - +
105A TRP* 3.6 39.9 - - + +
106A PHE* 3.2 36.1 + - - +
108A ASP* 2.7 41.6 + - - -
110A THR* 2.8 24.1 + - - +
111A THR* 1.3 76.4 - - - +
113A TYR* 1.3 64.4 + - - +
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Residues in contact with TYR 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER* 3.8 42.9 + - - +
3A ALA* 4.0 9.1 - - - +
4A PRO* 3.5 38.4 - - + +
68A LEU 3.6 6.3 - - - +
69A SER* 3.9 24.7 - - - -
105A TRP* 3.0 21.6 + - - +
111A THR* 3.6 35.5 - - + +
112A LYS* 1.3 75.0 - - - +
114A SER* 1.3 62.6 + - - +
115A ASN* 4.0 16.2 - - - +
146A PHE* 5.1 1.3 - + - -
166A ASP* 3.8 6.9 - - - +
523A PHE* 5.7 1.7 - + - +
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Residues in contact with SER 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLY* 3.0 25.6 - - - -
68A LEU* 3.0 27.1 + - - +
87A VAL* 3.7 17.4 - - - +
101A ALA* 4.3 3.6 - - - -
105A TRP* 3.4 16.3 - - - -
113A TYR* 1.3 68.9 - - - +
115A ASN* 1.3 61.5 + - - +
116A PHE* 3.6 8.6 - - - -
166A ASP* 2.7 29.8 + - - -
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Residues in contact with ASN 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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2A SER* 5.1 3.0 + - - -
3A ALA 3.1 21.8 + - - -
4A PRO* 3.4 9.2 - - - +
5A ILE* 3.3 40.3 + - + +
66A ASN 3.9 3.9 - - - +
67A GLY* 4.8 2.3 - - - -
68A LEU 5.2 1.0 + - - +
113A TYR* 4.0 13.2 - - - +
114A SER* 1.3 75.2 - - - +
116A PHE* 1.3 54.6 + - - +
164A THR* 2.7 32.6 + - - +
166A ASP* 4.5 2.4 + - - -
491A ILE* 3.6 21.5 - - + +
522A HIS* 5.2 9.1 - - - -
524A ASP* 4.2 12.5 + - - +
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Residues in contact with PHE 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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5A ILE* 3.6 8.6 - - - +
65A VAL* 3.7 28.0 - - + -
66A ASN* 3.1 27.3 + - - +
67A GLY* 3.4 33.2 - - - -
68A LEU* 4.4 0.9 - - + -
87A VAL* 4.0 18.2 - - + -
89A LEU* 3.8 15.5 - - + -
100A VAL* 3.7 42.0 - - + +
101A ALA* 4.0 12.3 - - + -
114A SER* 3.6 14.1 - - - -
115A ASN* 1.3 76.3 - - - +
117A GLU* 1.3 78.0 + - - +
124A VAL* 6.0 0.9 - - + -
164A THR* 3.5 13.5 - - - +
491A ILE* 5.1 0.4 - - - -
526A GLN* 4.7 2.5 - - - +
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Residues in contact with GLU 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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100A VAL* 5.9 0.5 - - - +
116A PHE* 1.3 87.9 - - - +
118A THR* 1.3 68.5 + - - +
119A ARG* 3.4 7.3 + - - +
161A TRP* 3.9 29.4 - - + +
162A GLY* 5.0 2.0 - - - +
488A PRO 3.9 5.0 - - - +
489A ASN* 3.5 14.0 - - - -
490A SER* 2.9 45.6 + - - -
491A ILE* 4.5 0.5 + - - +
526A GLN* 2.8 29.3 + - - +
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Residues in contact with THR 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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64A ASN* 3.7 37.2 - - + +
65A VAL 3.4 6.7 - - - -
66A ASN* 3.6 7.8 + - - +
116A PHE 3.5 2.4 + - - -
117A GLU* 1.3 76.7 + - - +
119A ARG* 1.3 63.1 + - - +
148A ALA* 3.5 18.3 - - + +
150A SER 3.7 14.2 + - - +
151A TYR* 3.4 31.9 - - + -
490A SER* 4.7 7.6 + - - -
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Residues in contact with ARG 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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64A ASN* 4.5 0.9 - - - -
65A VAL* 2.9 32.2 + - - +
89A LEU* 3.9 31.0 - - + +
98A SER 4.7 8.5 + - - +
100A VAL* 3.5 23.8 - - + +
117A GLU 4.1 6.2 + - - +
118A THR* 1.3 77.2 - - - +
120A PRO* 1.4 80.6 - - + +
121A ALA 3.4 1.4 + - - -
151A TYR* 4.6 0.2 - - - -
160A ARG* 4.6 17.6 - - - +
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Residues in contact with PRO 120 (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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62A THR* 4.1 15.7 - - + -
63A GLN 3.2 9.9 - - - +
64A ASN* 3.6 18.8 - - - +
90A SER 5.6 0.3 - - - -
91A SER* 5.6 3.3 - - - -
118A THR* 5.2 0.2 - - + -
119A ARG* 1.4 92.8 - - + +
121A ALA* 1.3 61.6 + - - +
151A TYR* 3.7 39.3 - - + -
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Residues in contact with ALA 121 (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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59A MET* 3.3 10.4 - - - +
62A THR* 3.8 7.7 - - - +
63A GLN 2.9 30.4 + - - +
65A VAL* 4.5 4.7 - - + -
89A LEU* 3.8 31.2 - - + -
90A SER 3.6 16.2 - - - +
91A SER* 5.1 3.1 - - - +
119A ARG 3.4 5.6 + - - +
120A PRO* 1.3 76.1 - - - +
122A ARG* 1.3 59.4 + - - +
123A TYR 4.0 6.3 - - - +
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Residues in contact with ARG 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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58A ASP* 2.9 34.5 + - - +
59A MET* 3.0 37.3 + - - +
60A LYS* 3.4 33.4 + - - +
61A THR* 3.7 21.8 - - - +
62A THR* 4.4 8.7 + - - +
90A SER 3.0 5.0 + - - +
91A SER* 4.4 10.5 + - - +
121A ALA* 1.3 73.9 - - - +
123A TYR* 1.3 91.5 + - + +
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Residues in contact with TYR 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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56A THR* 5.2 4.9 - - + -
57A ILE 3.3 5.6 - - - +
58A ASP* 3.5 33.3 + - + -
89A LEU* 3.5 4.9 - - - -
90A SER* 2.9 36.8 + - - +
91A SER 3.6 8.3 - - - -
92A ASP* 3.4 25.0 + - - -
93A GLY* 3.3 22.0 - - - -
96A TRP* 3.5 22.2 - + + -
121A ALA* 4.0 3.8 - - - +
122A ARG* 1.3 121.9 + - + +
124A VAL* 1.3 67.9 + - - +
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Residues in contact with VAL 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A TYR 4.0 0.7 - - - +
56A THR* 3.5 3.3 - - - +
57A ILE* 2.7 46.4 + - + +
59A MET* 3.8 26.9 - - + -
65A VAL* 4.6 1.3 - - + -
68A LEU* 4.2 22.0 - - + -
87A VAL* 4.6 3.4 - - + -
88A TYR 3.6 8.3 - - - +
89A LEU* 3.9 16.6 - - + -
96A TRP* 3.9 1.8 - - - -
116A PHE* 6.0 0.7 - - + -
123A TYR* 1.3 79.6 - - - +
125A ARG* 1.3 64.2 + - - +
126A LEU 5.2 0.2 - - - +
143A ILE* 6.2 0.7 - - + -
145A VAL* 4.0 35.4 - - + -
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Residues in contact with ARG 125 (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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54A THR* 3.5 26.3 - - + +
55A TYR 3.4 2.9 - - - +
56A THR* 2.9 24.8 + - - +
86A GLU 3.7 0.9 - - - +
87A VAL* 3.4 6.4 - - - +
88A TYR* 2.9 42.9 + - + +
93A GLY 5.0 2.4 + - - -
96A TRP* 3.4 61.9 - - + +
124A VAL* 1.3 80.8 - - - +
126A LEU* 1.3 61.6 + - - +
127A VAL* 3.9 16.4 - - + -
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Residues in contact with LEU 126 (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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53A HIS 4.0 0.5 - - - +
54A THR* 3.5 2.6 - - - +
55A TYR* 2.9 38.6 + - + +
68A LEU* 4.4 14.6 - - + -
70A MET* 4.4 5.2 - - + -
82A ILE* 4.1 15.0 - - + -
85A HIS* 4.1 13.0 - - + -
86A GLU 3.6 9.4 - - - +
87A VAL* 3.9 17.3 - - + +
105A TRP* 4.0 25.4 - - + -
124A VAL* 5.2 0.4 - - + +
125A ARG* 1.3 73.6 - - - +
127A VAL* 1.3 65.8 + - - +
128A ALA 4.1 0.4 + - - +
140A ILE* 3.9 27.6 - - + -
143A ILE* 4.0 17.9 - - + -
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Residues in contact with VAL 127 (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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52A PRO* 4.1 14.1 - - + -
53A HIS 3.5 8.1 - - - +
54A THR* 4.1 13.5 - - - +
85A HIS* 3.1 9.0 - - - +
86A GLU* 2.9 40.7 + - + +
88A TYR* 4.0 21.3 - - + -
125A ARG* 3.9 23.1 - - + -
126A LEU* 1.3 77.2 - - - +
128A ALA* 1.3 61.9 + - - +
129A ILE* 3.5 23.2 + - + +
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Residues in contact with ALA 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A PRO* 3.7 3.5 - - - +
52A PRO* 3.3 5.5 - - - +
53A HIS 2.8 32.8 + - - +
82A ILE* 3.9 25.6 - - + -
84A ARG 3.8 4.7 - - - -
126A LEU* 4.1 1.4 + - - +
127A VAL* 1.3 70.1 - - - +
129A ILE* 1.3 62.7 + - - +
130A THR 3.5 4.7 - - - +
131A GLU* 6.3 0.2 - - - -
138A THR* 3.5 33.9 - - + +
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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
------------------------------------------------------------
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